Thanks for your answer, Raze.
The user hasn't answered yet, but I have GOG Galaxy in suspicion. And after a short research it seems Galaxy considers modded game files as corrupted. I guess this isn't the case for mods in the regular documents mod folder, only files that are installed the pre-editor way in the 'Data' folders.
https://www.gog.com/wishlist/galaxy/dont_overwrite_modsOr did you launch via Galaxy?
