How to mark a thread as read in Lion Mail

It seems Mail 6.0 in Mountain Lion has fixed this for me. When I have new mail it shows as unread in both my in-box and my archive mailbox. And now, when I read it in my in-box it gets marked as read in both my in-box and my archive mailbox. Chalk one up for Mountain Lion.

Try these two solutions:

1. From the Finder, ⌥-click the Go menu and select Library whilst still holding ⌥.
2. Move the folder ~/Library/Mail/ to the desktop or another convenient location.
3. Launch Mail.app.
4. From the File Menu choose Import Mailboxes…
5. Choose Import Data from Apple Mail.
6. Navigate to ~/Desktop or wherever you moved ~/Library/Mail/ to.
7. Click on Choose.
8. Wait until it imports.

or

1. In a Finder window, navigate to ~/Library/Mail/V2/MailData, and delete any file that begins with Envelope Index, such as "Envelope Index" or "Envelope Index-shm" or "Envelope Index – awl". In my case, I had all 3 of these Envelope indexes, and moved them to the trash.

   Note: When accessing Library, keep in mind that your home Library is hidden in Lion. To access it, from the Finder, ⌥-click the Go menu and select Library whilst still holding ⌥.

2. Restart Mail. It will then rebuild a new list of messages, which can take some time, so be patient.

   Another note for Exchange users: After removing the Envelope Indexes, my Exchange account email content was blank. To revive it, I had to delete my Exchange email account and add it again fresh. After adding it from scratch (and the download took a while since I have about 12K messages), the mystery Unread Message notifications were gone.