I had a very similar experience. I had a backup from about 2 weeks ago and that restored fine, but I need a few e-mails I have received in the 2 weeks since. I have all the data available but unfortunately I have already downloaded new messages (I couldn't stop it, as soon as I restored my backup, it automatically fetched new ones as I have an always on LAN connection).
If I try and use the 'tools -> import messages -> from TB msg base v2 ' as you suggested, whichever folder I choose, it reports that 0 messages have been converted.
Please help. I am running The Bat! Pro Edition v3.71.03, and I am running with a an 'On-the-fly password'