I had the same problem once, seems to be some TB bug

First zip your whole mail folder to have a backup, also copy the account folder to another place.

Make a backup(Tools->Backup..), do not include 'Folders with messages' - it will be a small one
Delete the account (choose to remove files), close TB, and delete the account folder (if still exists under the mail folder).
Create a new empty folder named like the account , under the mail folder.
Open TB and create a new account, give it the same name, and for home folder select the empty one you just created (don't leave <default>).
In TB, in the new account create folders with same names as in the old account.
Restore the backup with settings (Tools->Restore..)

Now you should have an account that's like the old one, just without messages (and hopefully without duplicate folders).

Close TB, then put old message bases (MESSAGES.TBB) in each folder (overwrite if file exists).
Start TB and all should be OK

If I correctly remember , this was how I fixed it.
Assumes no encrypted message bases, attachments stored in message bodies - otherwise some extra steps may be needed.

hth