Oh God, that was just an example--Let me change my hypothetical situation: When I have the current pad/rotor combination broken in and all is well, I need to do some extensive maintenance on the wheel which requires its removal for a week (because I'm missing a part) and need to substitute my other standby wheel with a different rotor. Should I change pads and keep the first set for exclusive use with the rotor it broke in with?

I know, I should be able to foresee what parts I will need and therefore this situation should never arise, but hypothetically!!