Loser, only the eye-candy ones that do not affect gameplay. Altering them will not cause incompatibility when playing MP games, so changing them is IMO not a problem. But, it is best to leave all the files that will cause incompatibility with MP games alone. I am not advocating changing the eye candy files; just not changing the non-eye candy ones.
Of course, the AI files won't cause problems with MP games, but that is a different issue. I just suggest leaving the stock ones alone because you never know when you might need them again, and it is easier than having to reinstall the game to fix big mistakes you have made with them. Backing them up works too, ofc.