you shouldnt. or at least i dont think you do. its just a safe mode defrag i think. i could be very wrong though. but its not a system restore like you're thinking.
You need to do safe mode, then REBUILD the HDD Database. Mine was doing that and it fixed it without any problems. It doesn't do anything to your saves/trophies/games. Only thing it deletes is your messages.
You should give it a try, let me know how it goes.