Mail.app thinks I'm a new user
I don't think Mail has changed too much from 10.6.8 to now, but you should take my advice with caution, since I don't have the old system at hand.

Before starting this process, quit Mail. Any time you want to do a new test or reset to the existing state, quit Mail -- don't go copying or restoring things while Mail is running.

Now, copy your ~/Library/Mail and ~/Library/ApplicationSupport/Mail directory to a safe backup location. Also copy ~/Library/Preferences/com.apple.mail.plist. That should enable you to revert to the current status if something you try goes south.

I'm not sure what the ~/Mail directory is (I'm pretty sure I never had that in 10.6.8), but make a backup copy of it too.  It might be worth comparing that to ~/Library/Mail, especially the timestamps; if you're like me, it's likely an old copy.

Kent observed many corruption issues can usually be traced to a single file (~/Library/Mail/Envelope Index in 10.6). After you have the backup safely tucked away, you could try removing that file from the actual directory before starting mail for what follows. I think it will be regenerated, though that could take a while for big mailboxes.

I would then try setting up the user account. Either it will find the existing mailboxes, or destroy them. If it destroys them, you copy them back in from your backup, possibly delete the user, and try something else; or you can import the contents of those mailboxes. 

I don't have time to check it now, but this advice could probably be compared to advice for 10.6 by searching on mail issues for that OS. You could find out exactly where the various information is stored, I'm pretty sure.