I had a problem for months in Apple Mail (both on the Mac and the iPhone) where multiple folders would show up with an Unread mail count, even if all mail in that folder was already read. If you clicked one of the Unread folders, the Unread count would instantly go away. (But it would reappear when re-opening Mail.)
Here’s how I fixed it:
- Open Mail on the Mac
- Click on the Archive (or All Mail) folder
- Select all mail, right-click on the selected mail, and hit Mark as Unread
- Repeat step 3, but now hit Mark as Read
Now close and open Mail again and you will no longer see folders with Unread mail in them. If the problem continues to occur, you may need to repeat steps 2-4 on all of your mail folders.