For what it is worth, in my own limited modding experience, my best guess with this persistence issues you're facing is something wonky with a script, I had similar problems with spawning chaos in my old version of mod before rewrote script based on the recent update CA did themselves to it (fun fact, this game ran on the first game's invasion script till nearly end of its own development life span xD)

If its random, and save games are doing it something is borking the script when its loading out of these battles or something ( I know, SUPER helpful lol), but from using the script checker mod I think Vandy uploaded, I was able to trace where my mod was going wrong, or more correctly where my mod's script was conflicting with other things and just being skipped by the game's checks.

Fact people can fix this by reloading the game suggests it is script based as the fresh load is probably forcing your script to do all its nuts and bolts, vs being skipped when the conflict arises "in real time" ie, as the turn is ending and those checks are going on, now my script for example wasn't actually "broken", it worked on its own but the problem rose when I had it running with other mods, for some reason in my current version I lucked out and made it like most cross compatible thing I possibly could.

Anywho, my guess is script problem, maybe not necessarily something wrong with your script, just that like another mod, or something is causing this random conflict, especially if you're not seeing it testing the mod by itself, my money is on mod compatibility issues, specifically script related.

Hope that helps at all, lol more or less just top of my head but popped into the old brain pan reading through your comments, and sorry for just creating new thread but didn't want to spam your main front page.