Sorry for the double post, I can't seem to find an edit option. I just encountered this with Cassidy, and no matter what I do, 0000089.pro is coming back with a vengeance. I even had a save where the levelup persisted for one session, but upon restarting the game, he went back to his base stats. ProcessDat2 did nothing useful that I can tell. What did the trick was saving into a new save slot. I suspect this was the root of my problem, but my experience is limited and I could easily be wrong.