Rotors warp ever so slightly that you can't really see any difference but when you brake you can feel a good shake. Machining the rotors takes the warp out of the rotor. If you saw it done one time you would understand how it works. The only thing that can go wrong is if the warpage is so bad that you machine the rotor down below specs. But rotors can be had pretty cheap and it's probably worth getting new ones anyway!
-Andy
