you should be able to do it with out much issue but it the rotors are already going bad that might not be good for the brake pads

but either way it you sand the pad to open it back up it should seat to the new rotor

- 95 Mystique LS - Zetec/5spd - 99 Contour SeVT Sport - Duratec/5spd Official NE-CEG Contour/Mustang Family