Did you pick Aristocratic as a Feudal Theocracy? They no longer can use it, that might be the culprit. I doubt it has anything to do with national ideas, it's probably and incompatible idea group pick.
I doubt this, actually. It'd be really strange, because government changes don't replace idea groups locked to a previous government. Hordes keep Horde Ideas if they picked them, even if they change to a Monarchy, and can to my knowledge even stack them with Aristocratic if they like. I don't see why that should be different if Aristocratic was picked, but now Divine is offered - if anything it should just let them pick both, like in regular gameplay.
If two modifiers have been swapped around, though, the game might struggle, because modifier X is listed in the save game, but the idea slot is now occupied by modifier Y.
This is based on experiences I made when modding the game several years back. It might not still be relevant, but it strikes me as the likely culprit. Or it could be some unrelated string of code buried somewhere entirely unrelated in the patch - I had a few of those, too.
