Ich hatte hier vor einiger Zeit mal das Problem, dass ich bei AppleMail plötzlich immer eine bestimmte E-Mail als ungelesen angezeigt bekommen habe, obwohl diese selbst keine „ungelesen“ Markierung mehr hat. Folgender Eintrag aus Apples Supportcommunity hat mir dann weitergeholfen:

Guess what, i have the answer. go into the library folder in lion they make it so you cant see this folder. to get into it, go to your „go“ menu from finder with the option button held down and go to library, then go to mail, then go to the folder V2, then go to the folder „maildata“. move three files to your desktop or anywhere out of the way: „Envelope Index“, „Envelope index-shm“ and „envelope index-wal“. then re-start mail. it should fix the whole problem. It worked for me. after this, you can delete the old files from wherever you put them.

via Phantom unread emails: Mail shows 5 unread mess… | Apple Support Communities.