Hi Shezza,
if you do a factory reset through the menu and check all the options, yes you could erase your user files.
However, if you do the bootup resets, you will *not* lose anything. Now, which settings are you looking to reset?
If you're looking to reset to factory settings but keep song and registration memory active, hold the highest C while turning on your unit, and keep holding it (you'll see "Initializing system setup" on screen (when you see that text you can stop holding that key) and it will reset split point, effects, tuning, etc but keep all your soungs.
If you're looking to clear the registration bank? then instead hold the highest B while turning it on.
Mark