Could it be that your HDD got screwed up?
The program surely didn't delete 'em by itself.

Check if your MAIL folder still exists (possibly in C:\Program Files\The Bat!\MAIL).
If it exists, and its subfolders are browsable, try re-creating accounts as they were. (e.g. if you find folder "mail.beigetower.org", try to make new account with the same name, and all of the settings should be restored).

If not, try scandisking to fix the mixed-up chunks on HDD...