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As you can see from the screenshot, Mail has a problem with flagging emails. All emails in here were once flagged, but now only two of them actually are. Yet these emails persist in showing. Sometimes the total count is different to either number.

enter image description here

I have tried the basics: quit Mail, restarted my Mac. Any thoughts?

macOS 10.15.2

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• Quit Mail if it’s open.

• In ~/Library/Mail/V7/MailData, delete any file that begins with “Envelope Index,” such as Envelope Index or Envelope Index-shm.

• Your home Library folder is hidden by default. To display it, choose Finder > “Go to Folder” and then enter “~/Library”

• Open Mail.

• Mail creates new Envelope Index files. This process may take a few minutes, depending on how many messages Mail is reindexing.

• It will fix your issue.

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    Does this imply that the indexing was broken? would a spotlight re-indexing solve also the problem? – seralouk Nov 3 '20 at 13:29
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    Great, this deleted all my flags, not only the ones that are wrong. Would have been very useful to have a statement about that in your answer. Really annoying situation for me now... It seems I can't replace the newly created Envelope Index files with the ones moved to trash anymore. :-( – Joshua Muheim Dec 18 '20 at 13:06
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    UPDATE: I'm sorry, it indeed re-created the flags after a while, so my previous comment is not true. All good, just have some patience after starting Mail.app. :-) – Joshua Muheim Dec 18 '20 at 13:53
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Two things to try:

  • Find out which account they belong to, select it in the sidebar and rebuild the mailbox using Mailbox Menu. You would temporarily lose all attachments, and they'll be downloaded again.

  • If all the flagged emails have one color, select them all, and assign them a new flag.

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