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@LIAB, you said
I have a suspicion as to what happened. I was briefly using iCloud Drive to store my Desktop and Documents folder on at least one of the Macs here, but eventually turned it off because it seemed slow or unreliable. I can't recall what put me off exactly, it was some time ago. Anyway, everything that's corrupt is in the "Documents" folder on iCloud Drive, which I've been using to manually copy backups to. I'm thinking that the folder name has something to do with this... it's reserved for use with Macs that keep the user Documents folder on iCloud. Whatever happened, happened months ago because my backups going to November so far, which include iCloud Drive archives, have those same files toasted.
From the article from Apple, when. you turned off Desktop and Documents on whatever Mac you had it turned on, it created a new Documents folder on that Mac and inside that folder would be an "archive" but only if you chose to preserve the files. Note also that in the article it says (My bolding)
In the Finder, you'll see your Desktop and Documents folder in the iCloud section of your sidebar. If you add a second Mac Desktop, you'll find those files in the Desktop folder in iCloud Drive. A folder is created with the same name as your second Mac.
So any second Mac that you share that icloud with will be separately identified. Also in that article:
You can organize and combine folders from multiple Macs when you turn on Desktop and Documents on those computers too. After you turn on Desktop and Documents on a second Mac, you'll find its files in folders with the same name as your second Mac inside your original Desktop and Documents folders. Then you can combine your files manually, but iCloud doesn’t automatically merge the files in case you want to keep them separate.
So, the iCloud has a way to identify the Mac that first put the Documents folder in the cloud because it displays them differently on any Mac sharing that account. I don't use iCloud that way myself, but it would be interesting to see what happens when Mac A and Mac B both turn on iCloud for Documents and Desktop for the same Apple ID. I would bet that on Mac A there would be a folder named Mac B inside Documents and on Mac B there would be a folder named Mac A. What I don't know is what would be at the iCloud account. Two Document folders? Named Mac A and Mac B? Maybe somebody who knows will let us know.

What may have happened is that when you stopped using the folders from that original Mac, iCloud made note of the fact that those folders were no longer in use by any dedicated machine, which may have led to the issue. You put things in that folder that then became detached from any machine, as the folder was not attached. Had you turned on iCloud on your present machine, I suspect iCloud would have created a new set of folders, now attached to your system and those files could have been stored properly. Or if you had created a different folder at iCloud and put them there, they would have been preserved. But by putting them in these unattached folders, they got lost. Not much help to you at this point, I know, but a good thing to know for the rest of us.
 
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@LIAB, you said
From the article from Apple, when. you turned off Desktop and Documents on whatever Mac you had it turned on, it created a new Documents folder on that Mac and inside that folder would be an "archive" but only if you chose to preserve the files. Note also that in the article it says (My bolding) So any second Mac that you share that icloud with will be separately identified. Also in that article:
So, the iCloud has a way to identify the Mac that first put the Documents folder in the cloud because it displays them differently on any Mac sharing that account. I don't use iCloud that way myself, but it would be interesting to see what happens when Mac A and Mac B both turn on iCloud for Documents and Desktop for the same Apple ID. I would bet that on Mac A there would be a folder named Mac B inside Documents and on Mac B there would be a folder named Mac A. What I don't know is what would be at the iCloud account. Two Document folders? Named Mac A and Mac B? Maybe somebody who knows will let us know.

Explained here, with a screen cap.
Add your Desktop and Documents files to iCloud Drive - Apple Support

What may have happened is that when you stopped using the folders from that original Mac, iCloud made note of the fact that those folders were no longer in use by any dedicated machine, which may have led to the issue. You put things in that folder that then became detached from any machine, as the folder was not attached. Had you turned on iCloud on your present machine, I suspect iCloud would have created a new set of folders, now attached to your system and those files could have been stored properly. Or if you had created a different folder at iCloud and put them there, they would have been preserved. But by putting them in these unattached folders, they got lost. Not much help to you at this point, I know, but a good thing to know for the rest of us.

That sounds like my thinking here. Which is just crazy that it works this way if so. These iCloud Desktop and Documents folders, if intended to be tied to a specific machine, should be CLEARLY labeled as such, even if only enabled on one Mac, and siloed to their own sub-directory by machine id. Not dropped in the root level of iCloud Drive. A folder named “Documents” at that level logically should be a free-for-all.

edit: the screen cap from Apple’s page above just gave me an “aha” moment and refreshed my fuzzy memory. So the “Desktop” folder is a special one in the root level of iCloud Drive and has sub-folders that are machine-specific. “Documents” would be the same. So those folders wouldn’t have their entire contents synced across all Macs... just each own’s sub folder would be. Stop using that “Desktop and Documents” feature, and apparently the folder continues to act “special” like it’s waiting for a machine-specific sub-folder.
 
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Yeah, that's the same article I referenced and quoted from. It's curious if it works that way. I've never used it because I want to be able to get to my documents even when I'm not connected, but I do think that multiple machines using the same Apple ID should be distinguished at iCloud. As I said, maybe somebody who is doing that will tell us what it looks like when two machines share the iCloud.
 
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Yeah, that's the same article I referenced and quoted from. It's curious if it works that way. I've never used it because I want to be able to get to my documents even when I'm not connected, but I do think that multiple machines using the same Apple ID should be distinguished at iCloud. As I said, maybe somebody who is doing that will tell us what it looks like when two machines share the iCloud.

There’s a screen cap there demonstrating it. Here it is:

macos-catalina-finder-icloud-drive-desktop-documents.jpg
 
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Yes, but what I am wondering is what iCloud.com shows. You said you copied your files to the folder there, which was associated with the detached Mac. So my question is, what does iCloud.com show with two Macs using iCloud on the same Apple ID? Not through Finder on either Mac, but using a browser.
 
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Yes, but what I am wondering is what iCloud.com shows. You said you copied your files to the folder there, which was associated with the detached Mac. So my question is, what does iCloud.com show with two Macs using iCloud on the same Apple ID? Not through Finder on either Mac, but using a browser.

That’s not quite how it works. My memory was a little fuzzy but that screen shot jogged it. Here’s how this works, if I have pieced this back together correctly. When you enable “Desktop and “Documents” on iCloud, it creates first a “Desktop” folder and a “Documents” folder at the root level of iCloud Drive. Then, inside those folders, you get the Mac-specific folders. If you are on an iMac for example, the contents of the iMac-specific sub folders should show up and act like local folders, and synced behind the scenes to ~\Library\Mobile Documents as the local copy of everything. The contents of, say the MacBook-specific subfolders won’t sync in such a manner on the iMac, but can be accessed by going to iCloud from the sidebar and downloading (they actually get synced to that Mobile Documents location). You’d see a cloud badge signifying that the file needs to be downloaded.

So if you stop using the “Desktop and Documents” feature, those machine-specific folders go away and a local archive is made in your home folder. Those root “Desktop and Documents” folders, which themselves are not machine specific, don’t go away, but even though they look like a normal folder that you could have created yourself, anything you add to it stays there on iCloud only and doesn’t sync to any Mac automatically. All other content outside those folders, unless I’m mistaken, do normally auto-sync to the Mobile Documents as a local copy for offline access on all Macs.
 
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So, to be clear, you put these missing documents in the folders shown in the Sidebar of Finder. But after you disconnected the Mac that created them from iCloud? If so, I'm surprised the folders stayed in your Finder, unless you were not syncing that second Mac anymore.
So if you stop using the “Desktop and Documents” feature, those machine-specific folders go away and a local archive is made in your home folder.
From my reading of the Apple document, I think the local archive is made ONLY if you ask for it. The document says:
If you turn off iCloud Drive or sign out of iCloud, you have the option to keep a local copy of your files that are in iCloud Drive. Whether you decide to keep a local copy or not, a new Desktop and Documents folder is created in your home folder. If you choose to keep a local copy, your files in iCloud Drive are copied to a folder called iCloud Drive (Archive) in your home folder.
My emphasis there.
 
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So, to be clear, you put these missing documents in the folders shown in the Sidebar of Finder. But after you disconnected the Mac ythat created them from iCloud? If so, I'm surprised the folders stayed in your Finder, unless you were not syncing that second Mac anymore.

No. Again, I’m currently using the root-level “Documents” folder in iCloud Drive as a generic folder, which is not, was not, nor ever will be itself tied to a particular Mac. Only subfolders inside the root Documents folder get tied to a specific Mac. So, what I’ve been doing is I click on iCloud Drive, then Documents, and then add documents that I want to access across all Macs. I’m trying to use it as a master “Documents” folder that gets automatically synced for local offline access if need be, but it doesn’t actually work this way. Not this particular folder. Which is what’s so blasted confusing because everything else does! That’s how Dropbox worked.

From my reading of the Apple document, I think the local archive is made ONLY if you ask for it. The document says: My emphasis there.

That may well be, but irrelevant in my situation.
 
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AH, ok, the light finally came on. Yes, the Document and Desktop folders in iCloud are reserved, as it were, for use to unload the local Mac from having all of the documents on the local drive and as such, only sync with the individual Macs when they are, in fact, associated with those by turning it on. In your case, had you created a folder on iCloud named anything but that, it would be synced to any other machine, including iPhone and iPad, that used iCloud drive as storage. So, for example, a folder in iCloud named "LIAB" will sync to all accounts associated with that same AppleID and iCloud account. That's exactly how my wife and I share documents we both edit together.

That does not solve the zero length files, unless as you referred to earlier, you transferred an alias instead of a real file. But it does solve the sync issue for you. Just create a separate folder in iCloud for what you want to sync across machines. I tested it and you can drag that to the Sidebar to be available to you all the time. Dragging and dropping files into that folder then show up on all other linked devices where they have the little cloud icon, but can be downloaded. I set up a folder and put a file in then went to my iPhone and there it was!
 
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AH, ok, the light finally came on. Yes, the Document and Desktop folders in iCloud are reserved, as it were, for use to unload the local Mac from having all of the documents on the local drive and as such, only sync with the individual Macs when they are, in fact, associated with those by turning it on. In your case, had you created a folder on iCloud named anything but that, it would be synced to any other machine, including iPhone and iPad, that used iCloud drive as storage. So, for example, a folder in iCloud named "LIAB" will sync to all accounts associated with that same AppleID and iCloud account. That's exactly how my wife and I share documents we both edit together.

That does not solve the zero length files, unless as you referred to earlier, you transferred an alias instead of a real file. But it does solve the sync issue for you. Just create a separate folder in iCloud for what you want to sync across machines. I tested it and you can drag that to the Sidebar to be available to you all the time. Dragging and dropping files into that folder then show up on all other linked devices where they have the little cloud icon, but can be downloaded. I set up a folder and put a file in then went to my iPhone and there it was!

Bingo! Clear as mud, eh? So what I think the zero-byte files were are placeholders that exist in the Mobile Documents folder that is where the local copy of all files in iCloud are synced to. My guess here is that when I started using that Documents folder as I did, the placeholder files were put on the Macs so that they wouldn’t take up space, but otherwise acted like an alias would. Except opening it would actually force the file to sync to the Mac first so it could be opened. In the case of the normal use of the “Desktop and Documents” feature, if on your iMac and you went through your Mobile Documents folder and found the subfolders for your MacBook’s Documents, you should see all zero-byte files because they are not normally synced to the iMac. But you have to see something when you’re looking at the iCloud Drive directory in Finder. What most people don’t realize is that when you look at iCloud Drive, you are actually looking at the contents of Mobile Documents in your Library.

So anyway, what I think happened to me, is that when I.clean reinstalled Catalina and manually migrated back all my user data, I may have copied my Mobile Documents folder back over, not realizing that some of those files were not the actual full files. So when they synced back to iCloud, those placeholders overrode the actual files.
 
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Yes, I think the "fatal" mistake was the manual migration. In essence, to the OS you created a whole set of files with no content, which were dutifully synced to the iCloud. I suspect that had you used Migration Assistant, that would not have happened as MA should know the "files" in the Mobile Documents are not really files, just placeholders. Bummer, that.
 
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I believe users turn it off (mostly) because they are running out of iCloud storage space, and don't want to lose their data.
 
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Bingo! Clear as mud, eh?
... ... ...
What most people don’t realize is that when you look at iCloud Drive, you are actually looking at the contents of Mobile Documents in your Library.


Phew...!!!

I have a feeling that this similar topic will be cropping up for a few more times yet. :Smirk:

It's too involved for my old brain to sort out, but then I won't have to if I stay using Mavericks, besides I don't need the feature. But good luck to those who do.

BTW: Great sluthing and providing good translated Help for the feature and how it actually works correctly.





- Patrick
======
 
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Yes, I think the "fatal" mistake was the manual migration. In essence, to the OS you created a whole set of files with no content, which were dutifully synced to the iCloud. I suspect that had you used Migration Assistant, that would not have happened as MA should know the "files" in the Mobile Documents are not really files, just placeholders. Bummer, that.

Well as it turns out, my theory about the Documents folder being treated differently was completely wrong. I just a moment ago copied a file into the iCloud Documents folder on my iMac, then got my MacBook Air and opened it up. As soon as I logged in, I noticed the iCloud Drive icon in the Finder sidebar indicating it was syncing something. Sure enough, it was that test file I put in the folder from the iMac.

For some reason, iCloud is also not auto-syncing everything in the root folder like I thought it should be. I have a handful of items there that show they are available for download, and they do NOT show as having zero bytes. When I copy an "un-downloaded" file from Mobile Documents to another location in my user Home folder, it downloads to BOTH locations.

Now HERE is something interesting! There's a video I made that's on iCloud but not synced.

1: I took my MBA off wi-fi, then copied that un-synced video and pasted it on my Desktop. This action triggered the iCloud Drive icon in the Finder sidebar to indicate it was trying to initiate a syncing session. Since I was offline, it obviously could not.

2: The cloud badge is not present for the copy on my Desktop but is for the one in the iCloud folder. The Desktop copy also reads as 192 bytes in size, compared to 15.7 MB for the original but un-downloaded copy in the iCloud folder.​

3: If I try to run the copy on the Desktop, it fails, saying it can't be streamed. When I turn wi-fi back on, the original in my iCloud folder downloads and works. Nothing ever changes for the Desktop copy.

4: Moving the Desktop copy back to iCloud doesn't make it work again... it's corrupt. So... apparently if you copy a file from the local iCloud folder to another location while OFFLINE, the copy is toasted, but there is NO INDICATION that this has happened, nor that it shouldn't be done!​

5: I repeated this process with a small PDF file that hadn't been synced and had the same result. The "corrupt" copy also read as 192 bytes, so THAT is what a "placeholder" file's size actually is.​

So what I thought "may" have happened should have only if I had done this offline, and I most certainly didn't. Besides which, my corrupt files are 0 bytes while in this test, they appear to universally be 192 bytes. So unless my CCC backups that I worked with added another layer of complexity to this, then my theory is completely out the window. That's what I get for making theories in the middle of the night while low on sleep without my Mac in front of me to check myself. *facepalm* But this little test does provide some insight. I am also still baffled as to why some of my iCloud Drive files and folders are automatically syncing across my Macs while others are not. Clearly, from what I tried just a short while ago, they are SUPPOSED to, yet I have quite a number that aren't, and it's a variety of file types, smaller and larger. I feel like maybe there are some "legacy" issues in play here and I need to just download everything to one local location; validate it all; clear iCloud Drive; then re-upload. But I shouldn't HAVE to do this. Geezus Apple, get your act together.
 
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LIAB, you have used lots of variations of iCloud and iCloud drive to the point where I don't really know what you are doing. As I see it, there are three forces at play: iCloud Drive is a syncing folder on the Mac or iDevice where if you put files, they get synced up to the iCloud Drive in the sky; iCloud itself is a syncing service that can sync across devices logged into your AppleID for things like Messages, Mail, etc, and which can unload files in Documents and Desktop to the cloud service if you tell it to do so; and iCloud.com, where these various files and folders can be seen from any browser. So, you said
I just a moment ago copied a file into the iCloud Documents folder on my iMac, then got my MacBook Air and opened it up. As soon as I logged in, I noticed the iCloud Drive icon in the Finder sidebar indicating it was syncing something. Sure enough, it was that test file I put in the folder from the iMac.
By "iCloud Documents" folder did you mean a folder on the iCloud drive? Not sure what you actually did, but from the description that sounded like what you did. In which case what you saw is exactly what you should see.

For some reason, iCloud is also not auto-syncing everything in the root folder like I thought it should be. I have a handful of items there that show they are available for download, and they do NOT show as having zero bytes. When I copy an "un-downloaded" file from Mobile Documents to another location in my user Home folder, it downloads to BOTH locations.
What does "root folder" mean in that context? iCloud drive does not copy the root of anything, just what you put in the iCloud drive folder. Then it should sync up to the iCloud drive at iCloud.com and be available to any and all devices also logged into that same AppleID. The ~/Library/Mobile Documents is not meant for the user to manipulate, although you can do so. So when you copy something from that normally-hidden folder to your Home folder the download occurs because your demand for that file means iCloud has to copy it into the Mobile Documents folder for you to do anything with it and then another copy is put where you want it to be, i.e., your Home folder. That, too, is how it works.
1: I took my MBA off wi-fi; copied the un-synced file; then pasted it on my Desktop. This action triggered the iCloud Drive icon in the Finder sidebar to indicate it was trying to initiate a syncing session. Since I was offline, it obviously could not.
That tells me that in System Preferences for that MBA, AppleID, iCloud Drive, Options, the "Desktop & Documents Folders" is checked, that is to say, the MBA is storing the Documents and Desktop at iCloud, not on the MBA (unless you ask for them). The actual location in System Prefs is version-dependent, I described Catalina. I think iCloud was listed in Sys Prefs previously.
2: The cloud badge is not present for the copy on my Desktop but is for the one in the iCloud folder. The Desktop copy also reads as 192 bytes in size, compared to 15.7 MB for the original but un-downloaded copy in the iCloud folder.

3: If I try to run the copy on the Desktop, it fails, saying it can't be streamed. When I turn wi-fi back on, the original in my iCloud folder downloads and works. Nothing ever changes for the Desktop copy.
That looks like the Desktop copy is an alias to the one in the ~/Library/Mobile Documents. The filesize shown in the iCloud Drive folder is taken from what is reported as the file size in the cloud. But it's not the space taken up on the drive. And when you try to get to the Desktop copy when disconnected, it cannot stream the file down for you. So far, working as advertised.
Moving the Desktop copy back to iCloud doesn't make it work again... it's corrupt. So... apparently if you copy a file from the local iCloud folder to another location while OFFLINE, the copy is toasted, but there is NO INDICATION that this has happened, nor that it shouldn't be done!
Not toasted, just overwritten. And when you re-establish the connection, the new and unusable file is synced, so you lose the copy in the cloud. But again, that's how the system works. YOU put the link into the folder, so the system assumes you know what you are doing and syncs up that new, short file with the same name.

Not to be terribly rude, but the system is working exactly as you told it to do.

Consider this: the system does not know that the file on your desktop is not valid, nor that it is not what you really want. All it knows is that the file on the Desktop was moved into the iCloud folder and amended the existing file there. It could have been that you legitimately had a file with that name, worked on it using some application, saved it back to the drive and put it on the Desktop, realized you wanted it in the cloud so you copied it to the iCloud drive. Now what I think it should have done is to tell you that a file by that name already existed and to confirm that you wanted to replace it, but you didn't report that it did that. Did it do that, by the way? In any event, once the new file was saved in the iCloud drive folder, the system did exactly what it is designed to do, sync to the cloud so all other devices can now access the updated file. That is how it is supposed to work.

Apple has made it more confusing that it needs to be by sharing the "iCloud" term. Let me try to describe it by using X for the iCloud Drive folder, Y for the iCloud sync service and Z for the feature to store Documents and Desktop files in the cloud. For now I'll ignore Mobile Documents because that is not intended for users to muck with. So, you have turned on X and have a folder where if you put a file or folder it gets copied to the cloud (generic) and where any other machine using X can also get to that file or folder. That is kind of like Dropbox, or Google Drive, or OneDrive from MS. It works with or without Y or Z. It's just a file sync service so that all devices pointing to that X drive see the same version of the file last saved. The Y service syncs up lots of things, but not the files synced by X, except that the Z option is available as part of Y. So you can have Y with or without Z and you can have Y and/or Z without X. What Z does is to move everything from the Documents and Desktop folder from ~/ folder to the cloud and replaces them with links, saving space on the internal drive. But it doesn't copy or sync any of the other folder or files in ~/, just Documents and Desktop. (Thought problem; does it copy X as well? After all, those items are already in the cloud. I think it does, because Z is separate from X totally.) When the user wants a file and clicks on it, Z downloads it from the cloud and when it is saved back to the same folder, Z copies it back to the cloud, overwriting what is there if the name is the same.

So, in your example, you have a file you have copied to the Desktop, which got synced up to Z because it was turned on and connected. Then you disconnected, and what was left on the local Desktop was just a pointer file with 192 bytes. You then copied that 192 byte file into the X folder. At that point, as far as the system was concerned, you wanted to replace what was in X with this 192 byte file. Then you reconnected and everything synced up, which meant that the 192 byte file was sent to the X version in the cloud to replace the full file there. In your words, it got "toasted" because you toasted it. And since the X folder is included in the Z sync, as soon as you overwrote X and synced, Z got toasted as well.

How to prevent that? Well, what you can do is to keep X, Y and Z separated. Frankly, I don't use Z at all because, as I said, I want my files even when not connected, so I only use Z and Y. But if you do want to use all three, then be careful about how you move files from X to the folders synced by Z, particularly when offline. I would maybe even go so far as to create a new folder at the ~/ level, maybe called "Unsynced" and when I moved a file from X, put it there rather than in Desktop or Documents, where it gets synced by Z. Then I can edit and manipulate it from "Unsynced" until I get it finalized and then copy from "Unsynced" to Desktop or Documents or X, whichever I choose. If Desktop/Documents, then the Z process will then sync and overwrite the cloud version with the new and if X, the normal sync will to the same. Now you might argue that eventually everything you use will be in "Unsynced" and you would be correct in that. And that is an additional reason for not using Z at all.

And don't much with anything in ~/Library/Mobile Documents because that bypasses all the checks in the system, such as they are.

Is that any clearer, or have I fogged your mind completely?
 
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Is that any clearer, or have I fogged your mind completely?

No. Unfortunately it's getting way too difficult for me to convey what's happening here. I'd have to start over and in excruciating detail elaborate on the file/folder paths and whatnot, and I just can't be bothered at this point. Just know this... when I said "iCloud Documents", it's the "Documents" folder on iCloud Drive. Trust me, I have a pretty good idea of how this is supposed to work now, though what happened to cause some files to become 0-bytes and others to not auto-sync is a mystery. But clearly, everything is SUPPOSED to auto-sync. You can see that for yourself.

I could buy into the notion that some folders in iCloud should auto-sync while others are cloud-only (I may want to only store some files on iCloud to save space on my Mac, for example, and access only as needed. In other words, use it like an FTP server), but I see no way to force such an option or differentiate one if it does exist.
 
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But clearly, everything is SUPPOSED to auto-sync.
Not actually, but I won't go through that again.
I could buy into the notion that some folders in iCloud should auto-sync while others are cloud-only (I may want to only store some files on iCloud to save space on my Mac, for example, and access only as needed. In other words, use it like an FTP server), but I see no way to force such an option or differentiate one if it does exist.
Those both can be done. First, to make the system work like an FTP server, where some files are in the cloud and not on your local system, turn on the Desktop and Documents function under iCloud in System Preferences. Now all the files and folders in those two folders will be kept on the cloud server and only brought to your local system when you want them. Kind of like an FTP server, but with automatic up and down loads. What is put on iCloud Drive (which is separate from the other iCloud service) should be synced across any device using iCloud Drive. Any file/folder you want kept locally would need to be kept in a different folder at ~/ level. You could name that folder "unsynced" or "local" or anything other than Documents or Desktop. iCloud Drive will still work as advertised, syncing across all devices, but you may want to try moving the iCloud Drive folder from Desktop or Documents to the ~/ level as well, just to make sure that the Documents/Desktop process does not muck with the files on iCloud Drive.

Another approach is to turn off the Documents and Desktop option, but first copy all of the files and folders to a different temporary location because when you turn it off the files/folders in the Documents and Desktop folders for that machine in the cloud are lost and the process will create new Desktop and Documents folders for you in ~/. (The turn off process is supposed to offer the opportunity to "archive" the files into the new folders being created on your local drive, but I would do it manually, just to make sure.) Once you have the option turned off, copy the files and folders from where you put them (or from the Archive folders the process may have created) back to the new Documents and Desktop folders that got created on the local drive. Now none of the files or folders in Documents or Desktops will be synced to the cloud, except for what is in the iCloud Drive folder. Put into the iCloud drive folder files you want on the local Mac as well as in the cloud and on any other system that has iCloud Drive enabled. It works just like Dropbox at that point. And even if the iCloud Drive is on the Desktop, or in Documents, that one folder will be synced by the iCloud Drive process. But none of the others in Desktop or Documents. That end state is not exactly like an FTP server, but more like Dropbox or similar sync services. The beauty of this second solution is that there are no aliases being created and no file should be "toasted" in this setup. Only files you put into the iCloud Drive folder will be synced to the cloud.
 
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*sigh* That is limited to the machine-specific subfolders if you are using the iCloud Drive “Desktop and Documents” option. The subfolders. The ones inside the master “Desktop” and master “Documents” folders at the root level of iCloud Drive. I am no longer using that option on any Mac and there are no machine-specific subfolders on iCloud Drive. They don’t exist. I turned it off loooooong ago and copied all the contents back to their proper places on the associated Macs. If I currently drop a file in the “master” Documents folder in iCloud Drive, that file will auto sync to all Macs, DropBox-style. I previously assumed that wouldn’t happen, but I was wrong. Same if I drop one at the root level of iCloud Drive... the new file will propagate to all Macs. Not a placeholder, the full file. Despite that, I have some files spread around in iCloud Drive that are not synced across my Macs. It’s completely random. Synced and unsynced files reside in the same folders, even at root level. This doesn’t make sense. It’s chaos.

If I want to use iCloud like an ftp server so they reside only on iCloud, there should be a proper, INTUITIVE way to do it. Not by enabling a feature that I don’t otherwise want to use.
 
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I could buy into the notion that some folders in iCloud should auto-sync while others are cloud-only (I may want to only store some files on iCloud to save space on my Mac, for example, and access only as needed. In other words, use it like an FTP server), but I see no way to force such an option or differentiate one if it does exist.
Apple doesn't offer that, so anything to make it sort of work will be a kludge. If you want an FTP server, you will need to find a service that offers it.

The description of what you are seeing (drop a file on the iCloud.com and it propagates) means that the macs it is propagating to are still somehow engaged with the iCloud Documents and settings. There are lots of things to check, but I'm not going to enumerate them at this point.
 
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One final comment for others that may be reading this thread. It's related to this:
That is limited to the machine-specific subfolders if you are using the iCloud Drive “Desktop and Documents” option. The subfolders. The ones inside the master “Desktop” and master “Documents” folders at the root level of iCloud Drive.
On my iCloud drive, there are NO folders named Desktop or Documents. The only things in there are files and folders I have specifically put there to sync to and from my iPad and iPhone. As I said, iCloud drive operates separately from the iCloud Documents and Desktop option.
 

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