Gmail Badge won’t update: Apple Support Communities. Nice solution by Scott Nash. I wonder if this is a weakness with Lion Mail?

Ok.  With the help of tech support, I managed to fix this problem.  Since I’m clearly NOT a moron who just doesn’t know what I’m doing, I suspect it’s possible others might have the same problem.  The issue was the envelope index file in the library.

~library/mail/v2/mail data/envelope index

If you delete that file it forces a ‘deep rebuild’ that recollects ALL your metadata.  It does not have recall your data from the servers, just the hard drive so it’s pretty quick.  After about four minutes of rebuilding, all my stuff reappeared and the badges were correct.

This is similar, but more extensive than the ‘rebuild’ at the bottom of the mailbox menu.  That didn’t work, but this did.