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.
EP 1990 Mazda RX-7 (used to be STU until the turbo cars scared me away, and STL rotary cars require too much ballast)
ITS/T4 2004 Nissan Sentra SE-R Spec V
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