I didn't want to make a new topic, but I couldn't find a suitable one to place this.
After unpacking a pk3 into it's .ufo's (Correct directory structure, game ran with the .pk3 renamed/removed) I try to modify them to my liking (Loosened civilian deaths, weapon "Balancing" etc.). Files change ok, save fine, all that stuff. But once playing, whenever the game reaches a part where the change would have an effect, that part of the file reverts (Weapon is loaded, that weapons stats revert).
I don't know how it knows the original, as I have removed the old .pk3 entirely (And am loading from .ufo's) and I was wondering if there was a way to keep changes made? I just realised I didn't consider making the files read-only.
Edit: Ok, that was it, set files to read only, and it's fixed. Mods, delete if you want, otherwise maybe leave for future reference if others come across this.