Now that's weird. I had no problems transitioning from SoA to ToB and my party was intact. But I did have the SoA and ToB patches installed.
If you feelup to it, I'd suggest uninstalling BG2 (make a backup copy of your saves first) then:
1. Reinstall SoA
2. Apply SoA patch
3. Reinstall ToB
4. Apply ToB patch.
5. Restart game.
OTOH, you may wish to visit
Baldurdash and check and see whether they have a fix for this bug.