MAJOR HELP NEEDED! - re: 840GB of "Hidden" files and "Disk Error" due to iCloud Drive

1. I kept being interrupted by a pop-up menu stating that my system was out of resources, and said pop-up menu asked if I'd like to Force Quit any of the apps it was showing me in order to free up some resource.
2. It got to a point where this window was popping up and making itself the topmost window every 5 seconds or so.
3. I read somewhere that even though I have like 140GB free HDD space (which sounds like a lot), that because it is a small percentage of my overall 3TB HDD, that the computer might be struggling.
4. So, I decided to try to find a way to alleviate some of that stress by offloading some of the files on my computer.
5. I usually just dumped files onto an external HDD but started researching iCloud Drive.
6. The way iCloud Drive was explained to me was that it's basically Apple's version of DropBox. The way I view DropBox is that it is, primarily, off-device storage in the Cloud. Yes, it CAN sync with a device, and yes iCloud CAN (and is supposed to sync with all of your devices), but that iCloud DRIVE was off-device storage. I've, unfortunately, come to find out that that person's explanation of iCloud DRIVE was incorrect.
7. So, I signed up for 2TB of iCloud DRIVE space, and started the uploading process.
8. I noticed a little while into the transfer process that my HDD space was going DOWN?!, and wondered how this could be since I was offloading files to iCloud DRIVE, and should thus be freeing up space on my iMac.
9. While the uploading process was still going on, I started posting on a forum and someone finally explained that iCloud DRIVE is just a larger capacity storage option under the umbrella of iCloud and that the files remain on your computer. This is, obviously, not at all what I wanted.
10. So, I stopped the upload process to iCloud DRIVE.
11. I then went out and bought an external HDD and transferred all 840 GB of files to the external drive (from the iCloud DRIVE that was on my HDD).
12. I then deleted the 840 GB of data on my iCloud DRIVE, and then deleted my trash.
13. So, having deleted the 840 GB of files from my iCloud DRIVE, turning off iCloud Drive, and emptying my trash, one would think that my HDD would've gone from 140 GB of "Available" space to around 1TB. Nope. Still stuck at 140 GB.
14. So, I ran Disk Utility (in normal mode), and you can see that everything looks fine in the first 2 pictures (but I believe that's because Disk Utility is only showing me the startup disk:
    
    
15. I hit some more forums and looked for people with similar situations and found one where people were chiming in about having all sorts of large groups of files in weird places on their computers, and some mentioned having large "System" folders, when those are typically small.
16. I bought an app called DaisyDisk and used it to scan my iMac HDD, as an Administrator, and it found that my "System" folder was over 840 GB!!!
17. It would appear that my computer stashed the 840 GB of files that I told it do delete, here. That's the only thing I can think of. I mean, it'd be quite the coincidence to delete that amount of data and have almost exactly that amount of data show up somewhere else on my computer on the same day, correct?
18. So, one of the options on DaisyDisk is to be able to gain access to, and delete, files in the "Hidden" subfolder of the "System" folder. However, even DaisyDisk is saying that it can't let me do that, seen here when I try to drag the "Still Hidden" folder to the garbage in the lower lefthand corner of the picture.
    
19. So, I'm at a loss. I deleted (or at least thought I did) approximately 840 GB of data to free up space on my iMac's HDD and let it run a little more unencumbered and faster, only to have that massive amount of data transferred to a "System" folder that my computer isn't letting me gain access to.
20. The fact that DaisyDisk let others delete some of their "Hidden" files in the "System" folder, but I was being denied the same functionality got me to thinking about permissions, etc.
21. I then reboot my iMac into Recovery Mode.
22. I then run disk utility again, with these results:
    
    
23. So, according to Disk Utility in Recovery Mode, I have a Disk Error on both "disk0s2" and "disk1s2", and by fixing them it's going to wipe them both clean.

1. Can anybody tell me why this happened (since the drive was perfectly fine 3 days ago)?
2. Can anybody tell me how to get at those "Hidden" "System" files in order to be able to delete them?
3. If the answer it "Yes" to question #2 above, will that somehow resolve the problem and there will no longer be a Disk Error, and/or everything will go back to normal like it was 3 days ago?
4. MOST IMPORTANTLY...If the answer to #3 above is "No. You're screwed. There's nothing you can do at this point", am I understanding the Disk Utility results correctly, I can "Fix" both of the drives with errors on them, effectlively wiping them out and starting over, but I will be able to do this from a functioning OS X boot drive...in other words, if I hit the "Fix" button for both drives, my computer will fix those drives and not do anything to the boot drive that OS X is on, nor will I need to boot from another drive external to my computer during this whole process....correct? The last thing I want to do is "Fix" the drives that appear to have errors on them, wiping out all of that data, and also, in the process have to boot from an external drive or something (since I don't have the CD that came with the iMac, handy).

MacInWin said:

Mojave creates what are called snapshots for backup purposes. The snapshots are considered to be system files. I would suspect that your system is full of these snapshots. So, first thing is to look at the settings for Time Machine. Open System Preferences/Time machine and look to see if "Back Up Automatically" is checked. If it is, and if you do NOT have the backup drive attached all the time, then every hour a snapshot is taken. These snapshots are cleaned up when a backup is made and the snapshots are released. So, if your backup drive is not attached, attach it and let it back up (it will take quite a while if those 840GB are, in fact, snapshots). Or if that box is checked and you've NEVER done a backup, that can also cause snapshots to be created that will never go away until you DO make a backup. Frankly, I recommend backups for everyone, but it's up to you what you do.

Here is a thread here from a while ago with some information on snapshots: https://www.mac-forums.com/showthread.php?346378-What-is-using-up-all-my-memory&highlight=snapshots

Give that a look, read the entire thread before you do anything, there are good suggestions there. But read the entire thread to get a good understanding of what may be happening.

So, if snapshots is the issue, get rid of them by the methods suggested in that thread, then see if that drive recovers. If it doesn't, come back and we'll try something else. My money is on snapshots.

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harryb2448 said:

Odd my post about not using Time Machine was deleted.

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harryb2448 said:

Odd my post about not using Time Machine was deleted.

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ferrarr said:

Maybe download Maintenance, https://www.titanium-software.fr/en/maintenance.html, and make sure you get the correct version for your macOS version. Install it (you may be asked to allow the app to change files in the system folder), then run it.

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MacInWin said:

Also, you can see if the snapshots is the problem by opening Terminal and entering this command:

tmutil listlocalsnapshots /

The result will be a list of all the snapshots on the drive. If you get a long list, that is most likely the issue and the backup should fix it.

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usagora said:

By the way, you could use iCloud as off-drive storage as long as you don't have it selected under System Preferences > iCloud. You can upload/download through the web interface (www.icloud.com). To my knowledge, Drop Box is not off-drive storage...it works just like iCloud. Box Drive, on the other hand, is.

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MacInWin said:

Well, I think the disk error comes from a different source. The image of Disk Utility you posted has an option to "Repair Permissions" and that option has not been around in a long time, so the version you booted from to do that check is probably pre-APFS and cannot read the drive, creating the error message. The drive may well be fine. The Recovery partition appears to be an older version of macOS. You might look at Apple in the Support area to see if there is a process to update the recovery partition. I know CCC can do that, but there may be a way to update it without third party tools. If you cannot find that, then make a bootable external drive with Mojave and boot from it to run Disk Utility to test the APFS internal SSD.

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1. "Fix" the non-boot drives on my Fusion 3TB Drive (disk0s2 and disk1s2), effectively wiping them out. Now, this begs the question, are the "System" files/folder that is giving me the problem on the Boot Drive? If so, then "Fixing" said non-boot drives won't solve my problem, correct?
2. If the "System" files/folder IS on the boot drive, I can also do a clean install, correct?
3. IF I choose this later solution, the clean install, I don't need to do it from an external HDD, or anything like that, correct? The OS X operating system is already on my Fusion Drive and I would just have to boot into Recover Mode, Go to Disk Utility, Erase my Drives, Quit Disk Utility, then select Reinstall OS X....correct?
4. Futhermore, IF I do choose to do the clean install as mentioned above, should I "Fix" the drives before doing it, or will the wiping/reinstalling of OS X take care of that?

MacInWin said:

The drives you see in that old version of Disk Utility are NOT, repeat NOT, non-boot, nor are they damaged. The old version of Disk Utility does not understand the new APFS format that has been applied by Mojave. So there is ZERO reason to wipe them out, IMHO.

The System files are definitely on the boot drive, and the boot drive is one of those two the old version of Disk Utility is showing you. So if you do press on and delete those drives, you have wiped out all the data on them.

You can do a clean install, just not from wherever you ran that old version of Disk Utility. If that is in the Recovery Partition on the drive, it will not reinstall Mojave, but something older, much older, as that old version of Disk Utility has functions (relating to permissions) that have not been available for several versions.

Recovery mode, assuming that is where you got that old version of Disk Utility, will install only that old version, leaving you to go through the update process again to get back to Mojave.

I would not bother to try to "fix" the partitions with that old version of Disk Utility, and I really don't think they need "fixing" at all. It's the old version of Disk Utility that causes the supposed error, not the drive.

All that said, if you have a backup, you can reinstall Mojave on the drive completely by following the instructions here: https://support.apple.com/en-us/HT201372

That document shows how to make a bootable installer on a USB stick for Mojave, which is what you need. Create it, boot into it, then use Disk Utility to erase the drive, then reinstall the OS. That will wipe out everything on the drive, so make a backup first. Once it is installed, you can then use Migration Assistant at the very first time it offers, to restore from the backup. Some products, like those from Microsoft and Adobe, may need to be re-registered to work. The system files that are causing problems should not be brought back by migration.

It will take more than 1-2 hours to do all of this. Plus, by doing this you won't know what actually caused the problem, so it could return.

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1. When I upgraded to Mojave, it changed my drive format from HFS+ to APFS, and therefore the version of Disk Utility that came with my machine when it was new, didn't know that in the future (read: now) there would be such at thing as APFS, so Disk Utility is looking at APFS like a side dish it didn't order, correct?
2. I ran Disk Utility from the internal 3TB Fusion HDD that came with my machine, and therefore if I do a reinstall it'll install the original OS X that came with the system (I think, Lion), and then I'll have to spend time to upgrade to Mojave...but even though I'll have done that, the reinstall will give me the older version of Disk Utility, which will once again look at the new APFS format like a side dish it didn't order, and I might be left with more (false) "Disk Error" messages.
3. I can install Mojave from the link you sent me without having to do anything before hand (PROVIDED that I my current drive backed up via CCC, correct?).
4. I do this via a bootable installer I'm going to make on a USB stick containing said Mojave OS.
5. Here's where I need some clarification...

• Once I have booted from the USB Stick (which I'm assuming I do by restarting the machine in Recovery Mode, then selecting the USB Stick as the boot source, correct?).
• I then choose the Disk Utility (FROM THE USB STICK AS WELL, correct?)...
• Erase the drive(s)...
• Quit Disk Utility...
• Reinstall the (new Mojave) OS from the USB Stick...
• Use Migration Assistant to restore from the CCC backup...

• Will I need CCC to be installed in order to do this, or a clone is a clone and my iMac, now running Mojave, will have access to this clone?
• Will Migration Assistant let me pick-and-choose which files I want replaced (because in addition to NOT wanting the bloated "System" file replaced, there may be other large files that I don't reinstalled due to lack of use, and would rather just keep in the clone backup)?
• I'm supremely confident that this screwup was a result of iCloud somehow confusing my computer, as it would be almost statisitcally impossible for me to have deleted 840GBs of information on one day, and then have my computer not only suck the next day, but also have that exact amount of space clogging my "System" folder. So, when you say by wiping out the computer and doing a fresh install I won't know what exactly caused the problem, at this point I need my computer and my life back and much as I'd like to know the exact culprit, I just don't have any more time to spend playing Columbo.
• So, I'll wait for your confirmation that I have everything correct, and will then pull the trigger with the Backup/USB Bootable Installer/Disk Utility Erase/Reinstall OS Mojave/Migration Assistant process.