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Restoring the file system
What this does is restore your bootup code. It doesn't take long at all. You could do this in the recovery menu. If your ps3 freezes, a power outage comes while you have it on, or a game crashes, next time you turn on your ps3, a message prompting you to do this pops up.
Restoring the database
This can only be done from the recovery menu & takes more time than restoring the file system. Doing this results in less freezing, quicker trophy sync times and, games & other apps running smoother.
There are a bunch of tutorials on how to get to the recovery menu so I will not include that here. Just google it

Hope you found this useful. Thanks for reading!
On another note, it would be a good idea to do both of these before installing any CFW and/ or if you have a large hard drive that's almost full.