Some of my mods are interface mods that change the checksum, so I disabled them all to retest. However, even with no mods enabled, my checksum in game is ba12, not 9b1f as expected. So my issue may be a result of a mod that won't remove.
I've not edited any game files outside of the mod folder. I'm going to uninstall, clear the folder, and start over with a fresh install and then try again.
make sure to use the clear button in launcher too just in case there are files elsewhere that wont get removed during reinstall
It was the clear button. After uninstalling, deleting the folder, and re-installing, it was still giving me ba12. But the clear button brought me back to 9b1f.
I loaded my original save, advanced one day, and saved again so I have a save without any warnings about missing mods.
The issue did not occur in multiple attempts, so I'm thinking it must have been something in my cache.
One potential culprit:
I had stopped using the Immersive Cities mod (adds unique pictures for many of the capitals) because it was showing strange terrain bonuses in the division designer (see attached phot0). It would show the river picture for many of the terrain types but the mouseover tip was "Hills". I assumed it wasn't an issue for the disappearing divisions because I had disabled it, but maybe it caused a change to the user folder that created the problem. I tried enabling it again, and I still get the strange terrain bonus displays & names in the division designer. It has also changed my checksum this time- not initially, but after I enabled/disabled it a couple times.
However, I could not recreate the disappearing divisions error- at least not with this save. I'll be removing Immersive Cities and clearing user cache. If I get any repeats, I'll try and get saves before and after.
Edit: added screenshot of Immersive Cities Mod impact on division designer terrain bonuses. Given the other reference to strange terrain bonus numbers, it's possible this one is the cause, or at least points to a portion of the code that could be doing something wacky.