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In Lion and Mountain Lion Mail, the "Mailbox List" included an entry for flagged messages, with an sub-entry for each kind of flag. This appears to have been removed in Mavericks Mail. Is there a (perhaps hidden) setting to restore this, or is it gone; and if so, how can I get a list of my flagged messages (of each kind).

I've tried creating a "Smart Mailbox", but that doesn't seem to work.

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I had this problem -- the "Flagged" folder disappeared from the Mail app and no longer contained any flagged messages, even though I could see that my messages still had flags if I logged into the iCloud website and looked at them there.

For me, the solution was to rebuild my Inbox in the Mail app. Select the mailbox you want to rebuild ("Inbox" in this case), go to the Mailbox menu, and select "Rebuild" at the bottom of the menu. It could take a minute or two, depending on how many messages you have. Suddenly Mail recognized all the flags again, and my Flagged folder re-appeared with my flagged messages in it.

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    This works in part: It appears that flags behave like smart mailboxes or as a kind of "hidden" or built-in Rule. By selecting a folder or a set of messages and re-running rules, I can get flags to appear in the "Flagged" list — but only the selected messages. I can also get a flagged message to appear in the list by clicking it. However "Rebuild" only finds the flags in my inboxes; there seems to be no way to find the flags els were, except using these "manual" methods. – orome Oct 27 '13 at 21:55
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Select the inbox in question, then the mailbox menu and "rebuild". We had this issue on 3 machines in my office and length rebuild was required. I've noted the flags show up if you surf to one of the flagged emails...it's as if "touching" the emails is required for the data to be triggering the flag functionality...rebuild must have the same effect.

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    Yes, I discovered the same. But this seems not to work by Mailbox, but by folder, of which I have several dozen. So this approach is a bit tedious and error prone. What I'd like is a way to rebuild the flags for all my mail at one go. – orome Nov 16 '13 at 15:06
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The flagged message folder isn't missing on any of the 5 Macs I have upgraded to 10.9 so I'm concluding that the folder isn't intentionally being removed as a matter of design.

I suspect you have some database corruption or another error (perhaps gmail two factor authentication) causing the missing folder.

Have you reached out to Apple support? They typically offer free support within 90 days of any "purchase" and it would be interesting to see how they handle a "purchase" for a free app.

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    Indeed, after about 4 hours, the list appeared with a single entry; now, overnight, two more have appeared. It seems the flagged messages are very gradually being found. But at this rate it will take several days for them all to reappear. Is it meant to take that long? Is there something I can do to accelerate the process? – orome Oct 23 '13 at 12:00
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    I've from 2 to 4 now. – orome Oct 23 '13 at 18:24
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    It could also be related to changes in how gmail and mail app work - have you ruled out gmail's custom IMAP settings and a bad interaction / long slow sync? – bmike♦ Oct 23 '13 at 19:02
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    Possibly. Would disabling any Gmail accounts do the trick or would I need to delete them entirely? – orome Oct 23 '13 at 19:24
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    I stopped using gmail with my Mac mail client about 8 months ago, so I have no real experience but my guess is that either would remedy things long enough for you to determine if the rest of your mail services are behaving properly. – bmike♦ Oct 23 '13 at 19:28
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The databases associated with your mailboxes are probably corrupted and need to be rebuilt. Simply choosing "Rebuild" from the "Mailbox" menu is worth a try, but is unlikely to do the trick. If it doesn't, the following steps will fix the problem:

  1. Quit Mail.
  2. Remove all of the "Envelope Index" files from the ~/Library/Mail/V2/MailData/ folder by opening the folder in Finder (⇧+⌘+G) and deleting all files whose names that begin with "Envelope Index". After deleting these files you should "Secure Empty" the Trash to be sure they're gone.

  3. Relaunch Mail and wait. This will take quite some time: many hours if you have a lot of messages.

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  4. Once Mail is fully launched, search your mailboxes (⌥+⌘+F) for "flagged" messages and wait again.

    enter image description here

    This can also take a surprisingly long time during which it will sometimes appear that nothing is happening, but patience will be rewarded as your flagged messages begin to appear.

Depending on how serious and extensive your database corruption is, it's possible that not all of these steps is needed. You might simply try the last step alone and see if it works. However, the missing flags are likely a sign of a problem that will manifest itself in other ways, so the surest approach is to do all the steps above.

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My flagged messages also disappeared, but they showed up again by themselves as I was reading this page. Seems to have "rebuilt" themselves.

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    Welcome to SE. This should be a comment (use "add comment" in response to the original question) rather than an "answer". This will probably be deleted. – orome Nov 4 '13 at 12:21
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Rebuild Mailboxes didn't work for me, but it turns out flags are actually part of Spotlight. I forced a re-index:

  1. drag the drive where your mail folders live (usually your boot drive) to the the Privacy tab in System Preferences → Spotlight.
  2. log out, log in.
  3. drag the drive back out of the privacy list and wait while your Mac re-indexes.

I found I also had to sort my mailboxes by the flagged column, then click on each flagged item in turn.

This solved my issue, and is mentioned in an Apple discussion here: https://discussions.apple.com/thread/5479534

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