I've had similar issues myself. Combat Abilities, Civil Abilities and Talents resets whenever I go back into a campaign, be it to continue working on it or continue playing it. I've not seen any Spells being reset, these seem to stick as is.
Combat Abilities, Civil Abilities and Talents are also reset whenever an NPC changes level. This might be what previous posters have experienced - even if you've a saved character, say a level 5 bandit which you've given +2 scoundrel and The Pawn, everything is reset on it if I spawn it at any other level, say 4 or 6 when trying to manage the difficulty.
What I've recently found out (while posting this as I wanted to test it before posting) is that it appears that NPCs seems to retain the changes the ~first~ time I reload the scene after having made changes. I made changes yesterday, went in now to see if changes were still there, and they were. I reloaded the game again, and it was gone in the scene I checked. However, in a scene I didn't load during the first loaded game, changes were still there. And then loading up the game a third time, changes were now gone in that second scene as well.
Currently, the method of saving the NPCs and replacing them once the players enters the scenes seems to work for me. It's very tedious though and certainly very frustrating for the players what with all the waiting.
In order to combat the level changes resesting the NPCs, I've started saving the same NPCs with several levels. This also works for now, but again, very tedious.
This is a major concern for me as the GM-mode is the only thing holding any interest for me in this game.
