Yeah, that really shouldn't happen...
If you mail Larian about it, you can send your save file to them with the analysis tool
http://www.larian.com/OriginalSinAlpha/AnalysisTool_DOS.exe , they'll look for what's wrong here and might even be able to fix this so you can keep playing.
I had minor things carry over with an earlier version (playtime and such) and they suggested I should fully close the game before starting a new one. This might work here as well, but you probably don't want to do everything all over again.