Like others, I'm no expert. I have, however, run different pads on the same rotors (I was trying out several different kinds of street pads to see if there was any difference...sounds like what you're doing). I asked around before I did it, and the answer I seemed to get was to scuff the rotor with sandpaper between pads. I did this and it worked fine. I never tried it without scuffing the rotors, however, so I don't know if anything bad would have happened.