Originally Posted by Von Manteuffel

Welcome aboard, werwil0.

If you use JSGME, you don't need to back-up the files which a mod changes. It does that for you. When you disable a mod, the files revert to how they were before you enabled it.

If you install a mod manually, before you copy the mod files into the appropriate folders, just make a new folder in the SH4 main directory, or in data and call it "BackUps" or "Originals" and copy the files into it. They'll sit safely there in case you need to restore your game by deleting the ones you've modded and copying the originals back. The presence of "BackUp" or "Originals" folders doesn't affect the game, since they're simply not recognised and so ignored.