Is Tb still trying to show your accounts, but did it change your mail directory?
If so you could try to change your mail directory back to it's location on your mobile drive.
You should do that by changinging the key
HKEY_CURRENT_USER\Software\RIT\The Bat!\Working Directory
in your registry.
If this won't work or you don't like to edit your registry manually you can do this:
Open TB
Delete any 'replaced empty accounts'
Create new accounts with the name of your old accounts and tell TB should be located on your mobile drive.
(TB should take the settings from your old account as long as your mobile disc is connected.)