Copy the file, make mods to the copy, delete or move the original, rename the copy back to the original name.
Windows doesn't want original files modified; hence, virtual store and the like. The above is a way to avoid virtual store. You should find your previously modded files in virtual store, it is a hidden folder, you will have to changed your folder options to find the virtual store folder.
Windows is trying to save the user from themselves, they think most users are idiots, they say it is a security thing, it just makes intelligent people angry.