Nop, the "restore filesystem" is basically the same process you see when you force a software shutdown... you know that screen that tells you "the PS3 has been turned off incorrectly and is needed to check the hdd"... and after that you see a horizontal progress bar that should take around 5 minutes (as most) to complete
If it takes more than 5 minutes is because the internal hdd filesystems had a big problem
And it doesnt deletes your files, incase there is some file orphan , or damaged it tryes to restore it (and incase is imposible to restore the damaged files then yes... that file is deleted because is the only thing that can be made with a corrupted file)
Is basically the same than doing a "checkdisk" in microsoft windows, it helps to keep the filesystems healthy, i use it a lot
--------------------
Edit: ops, sorry, i misunderstood you because the screenshot had option 3 hightlighted (and option 5 outlined in photoshop)
What i said applyes to the "restore filesystem", sorry