To fix that issue.
1) Quit Mail.app
2) Stop, Clear, and Restart your Spotlight indexation. To do so : https://support.apple.com/HT201716 OR
- Open Terminal.app
- Stop and Flush Indexation
- sudo mdutil -i off -E /
- verify the status
- sudo mdutil -s /
- Restart it
- sudo mdutil -i on /
- verify the status again
- sudo mdutil -s /
3) Clear the Mail.app indexes. You will find some "Envelope Index*" files in your ~/Library/Mail/V7/MailData folder. Trash them and empty the Trash. (They will be rebuild after relaunching Mail.app, don't worry).
To do so:
- From the Finder > Goto Menu > Go to folder: "~/Library/Mail/V7/MailData".
- From the Terminal.app: "open ~/Library/Mail/V7/MailData" (then Enter)
Restart your Mac. Re-open Mail.app, and all we be fine again.
PS: You need all those steps, and in this order ;-)