Merge update ruins storage filters

TL;DR
1) Deactivating the DLC did not deactivate the DLC
2) storage filters changed (selected items in conveyor loader and storage bins etc)
3) no changelog of changes to base game
4) DLC stuff added to base game that shouldn't be there (e.g. mentions of radiation and cobalt)

I recently bought the DLC and steam automatically installed it, but i first wanted to play some more on the base game. After starting the game i could not start any of my existing saves, so i deactivated the DLC. After the restart i could load the latest save without issues. I expected none of the content from the merge update to be active after deactivation the DLC, but this was not the case. I soon noticed some broken setups and new research steps.

Turns out some of the item categories changed a bit, which (probably) messed with existing containers. For example, multiple conveyor loaders that used to request egg shells, now requested all organics. This includes Slime that got transported all over my world, breaking a vacuum and other rooms' atmosphere. The same happened on Storage bins requesting egg shells. It seems to have also happened with ones that used to request sand and now also request regolith. There might be more.

Secondly, some resource disappeared from the filters as if i never discovered them. For example Niobium was non longer assignable in storage bins. When i cancelled the Thermium job in molecular forge, dropping the little niobium it contained, it appeared again.

I tried looking for some kind of change log for the merge update but it doesn't exist. There is a url in the patch notes, but it doesn't work ( it says "You do not have permission to view this content"). I'd like to know which of my setups no longer work before they ruin the whole experience. It was quickly clear that deodorizers now need power, but what else changed?

after a while the game crashed, see player log. I do not know what i was doing exactly.

Overall this has been a very disappointing experience! I'm ok with ignoring minor visual glitches (and i did) and even the occasional crash won't stop me from playing. But breaking changes to save games without a way to disable the changes or even know what changed i simply unacceptable.