unflagged emails stays in flagged folder

Yes, the Flagged folders only appear when there are emails that are flagged with any of the available flags. If you have more than one colour of flag applied to emails, then you will get a arrow-expanded list of those flags in the sidebar.

This is incidental to the bug. The bug itself, is that the index is not being updated when changes are made to Flags. We can use various manipulations to trigger it, but Quitting and Relauching Mail isn’t one of them ... Moving Flagged messages to another folder, does trigger indexing. Conversation and Related Message settings seem to be implicated too.

I had this same issue and I managed to resolve it by moving the offending message to a different email account, and then moving it back. It no longer shows in the flagged folder.

Apple doesn’t routinely monitor the discussions. These are mostly user to user discussions.

Send Apple feedback. They won't answer, but at least will know there is a problem or a suggestion for change. If enough people send feedback, it may get the problem/suggested change solved sooner.

Mail Feedback

Same here. High Sierra, iMac 27".

Deleted flag, no dice. Dragging flagged mail into any other mailbox except where it came from deleted the flag. Then dragged it back to the folder where it belonged.

Annoying, but it worked for me.

SDG

You can report the bug here: https://developer.apple.com/bug-reporting/

Does quitting and reopening Mail help?

If you un-flag the mail an empty folder having flagged icon empty folder remains in the side bar sometimes quitting the mail application doesn't remove it , again open mail application , quit for the second time the folder disappears .

If you feel that this is a bug a link is there https://developer.apple.com/bug-reporting/

Also send a feedback Feedback - Mail - Apple

Maybe try to unflagg the mail in your flagged folder one by one. I think the counts error is because you have flagged mail reply and received more than once. It is going to add the flag up every time you have it back and forth after you flagged the mail.

I've been fiddling with this problem too. It seems to have something to do with the Conversation setting being applied and all email flags not being cleared correctly on a Conversation. At least, that's where I've got to so far. Very annoying. As suggested, moving the emails to and from a different folder, updates its flag.

Monday will see the release of 10.14. Perhaps it will have been fixed.

Same issue here, for me ever since upgrading to High Sierra. Sent info all the way yup to Engineering at Apple and now can't get a hold of my third senior advisor on the case. Rebuilt Mail and went deep to disconnect Spotlight and restart that process, as it's the programming around Spotlight that keeps track of theses issues as I understand it. All temporary fixes as after a few days or now minutes, Flagged email folder is out to lunch. Frustrated as i like Mail's simplicity and I use Flagging for my business. Will report again!

After writing that reply, maybe, just maybe, bugging the debuggers enough and they released a fix in this latest macOS. It’s not the first time constant calling has not had proven results for me, going back to pre iCloud and iWork days.

FYI - I have tried Bandaid #3 - When I exit the flagged folder and then return the emails repopulate. This is all very annoying.

Bandaid 3 - right clicking on the rouge email and moving it to it's original inbox (which it shows it's already in), will almost always cause it to disappear from the flagged folder.

Apple,

Have you a bug on this issue? It's very annoying, and all listed workarounds are painfully time-consuming.

If you want others to take your products seriously, you should avoid/fix bugs like this.

I have the same problem and quitting and reopening does not change anything.

I have unfledged the emails in the stream one by one and the emails remain in the folder. Do you have another suggestion?