Ok, so if it wasn't the bbudgetenforced variable, I think it can only be one other thing.
The way I understand it, for the Shepherd character only, the game calculates how many points he should be able to have, based on what level he is, and if his total skills upgrades exceeds that many points, it resets all his skills, and gives him all the skill points he should have earned for his level.
I was dumb enough to change two things in the Coalesced.bin at the same time, and I assumed that the budgetenforced line was the one that fixed it. Since it's not, I think it's this:
Using the Coalesced.bin editor, go to biogame.ini/sfxgame/sfxgameconfig
and find the field 'levelrewards'
It's a list of how much exp you need for each level, and how many skill points you and your 'henchmen' get.
Edit the TalentReward= line for the next level you need, adding as many points as you want, and do the same for your team members using the HenchmanTalentReward= item.
Upon your next level up, you'll have a lot of points, and they should stick.
Note, it may work to edit the point levels for a lower level than you already have, thus increasing the limit of points when the game calculates if you've exceeded your points and preventing it from resetting the skills. I can't confirm this, however.