Mail issue with Flagged emails

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Mail 6.5 OS 10.8.4.

I had an issue with my Mail server / ISP not connecting. During the connection failure attempts all of my emails in the Inbox disappeared. I eventually had to delete the Account and create a new Account. It then download all of the emails that were on the Server.

I had quite a few emails "red flagged" in the Inbox and these were important to our business.

Now all of the newly downloaded emails are not showing any as being flagged. I went in to Time Machine and the recent, hourly backup shows all of the Inbox but does not have the Flagged Folder.

I'm assuming there is nothing I can do at this point but thought someone may know why the Flagged folder is now empty and also does not show on the Time Machine backup. Just for my own education.

And I am also curious of why my Inbox went empty just because I could not connect to the ISP server.

Is there any "maintenance" I should do with the Mail app? And is there a way to make a backup of the Flagged folder?
 

chscag

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It may be a matter of procedure. Open your mail program and bring the Flagged folder in view. Now enter Time Machine. Your backups should now show the Flagged folder. It might be possible to go back far enough to retrieve the flagged email messages.

I have had to use the above to retrieve lost email messages and or folders. Just opening Time Machine without the mail program open and in view, does not work to locate lost messages.
 
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Thanks, but that did not work. I had the Mail app open. I then opened the Flagged folder and then entered Time Machine. The Time Machine backup shows all of the Inbox, and all of the other folders, including other custom folders I created but not the Flagged folder. I'm starting to think the Flagged folder is actually part of the Inbox. Like a "mirror" of the Inbox but just segregates the emails you place a red flag on. Now I'm not totally clear on the difference between "Mailboxes" on the top, with Inbox, Flagged, Sent, Junk, and Trash folders under that heading, and then on down I have my Smart Mailboxes, and below that a heading "On My Mac" with custom Folders I created listed there.
 

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