Yes! Welcome to Divinity: Original Sin modding, a game where you can't actually activate mods after starting a game and saving it!
Even if you activate your mod in the main menu of your profile, when you load, it'll default to whatever mods is loaded for that specific save. Yes, there's a reason modding isn't a big thing with D:OS.
There's a workaround, though.
First, create a new game with the mods you want to use in your save. Save.
Use Lstools to extract both saves.
Delete the old meta.lsx from the save you want to modify, and paste the new meta.lsx from the recently created save.
You don't need to recompile the save. The game can actually load extracted saves just fine, as long as they're in their own folder.
So why does the meta.lsx sit there and screw with people? Why are saves even compiled and locked? No-one knows. Why does mods work like this? No-one knows. Welcome! *bops head with inflatable hammer*
