if it crashed during backup, the backup file is likely corrupt.
Anyway try the following:
Missing messages may have been deleted, not completely lost.
Select Inbox folder (or the folder messages were in), then click Folder menu / Browse deleted messages.
If you see the messages they can be restored.

If the above doesn't work (because you compressed folders, or for another reason),
install theBat on another computer / virtual machine, and try restoring the backup there.
In case of success export/import missing messages, or just move the message base files (MESSAGES.TBB).

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To avoid problems like this, I don't use theBat itself to make backups.
It's a much more reliable backup method to just zip or rar the entire mail folder, or desired parts of it. In case of a mess you can easily restore individual folders, only settings, everything together etc.