Had the same issue
I'm lucky I had only one user with this issue- a server with about 100 users was powered down 'uncomfortably' two days ago, so fortunately this is the only one I've seen so far. But, if it helps anyone else, here's what I did-
I have Webmin with Usermin installed, so there's an easier way to handle this:
Oddly enough, when I had this problem I could see my user's mail in Usermin or Webmin/Read User Mail, but not via POP/IMAP or Squirrelmail
So, logged in as the user in Usermin, I made a new folder, and copied all the mail to the new folder.
I then removed the 'inbox' directly out of the /var/mail directory, created a new file and did a chown to match the old one.
I restarted postfix and dovecot but I don't know if that will be necessary or not.
The process took mere moments once I figured out what to do.