I posted the following in another thread recently.
Brake material is transferred from the pad to the rotor and it is this pad material to embeded pad material friction that does the braking. This is what you're doing when you 'bed' the brakes. You're loading the rotor with pad material.
When you change pads to a different compound you need to clean up the rotors so the embeded material, that doesn't match the new pads, is removed. It's simple to do. Either turn the rotors (only if required for another reason) or use emery paper (or fine sandpaper) and scratch the surface entirely until it changes color. Then go ahead and re-bed the new pads.
I've pasted the following from the Hawk Brake site:
Clean a used rotor surface with fine sand paper or steel wool, rinse with water, dry and install before bedding new pads.
And:
Correct brake pad break-in (bedding) is important to assure quality braking performance over the life of the pad. This procedure allows the rubbing surface of the brake pad to slowly be brought up to racing temperatures. Proper bedding creates a transfer layer film of friction material to be applied to the rotor surface. This allows the brake pad material to rub against itself rather than the bare rotor. This increases the stopping performance of the brake pad and can reduce pad and rotor wear.
I've done this for years on all my race cars (and motorcycles) with success.
Greg