Have you noticed strange behavior on saves created with Dragonborn or one of the other DLCs if you go back to that save without them? I've noticed mammoths and netches appearing, sometimes in very strange places like interior cells, when I enter them. I thought it might be a mod I'm working on but I think now it might be the save that is the trouble.

It is never a good idea to remove a mod or DLC during a game. Scripts are baked into your save in this game. Removing the mod that put them there can cause your save to bloat. And save game bloat can cause all kinds of problems.