Situation: Bike needs new pads badly (they don't grip well, contaminated, or something). They might as well be wooden blocks. I ordered new pads, ended up with two sets of rears, and one set of fronts.... don't ask. Anyway, I've ordered another pair of front pads, but is it ok to swap one set of pads, let them bed in, and then swap in the other? Both front rotors are bolted to the same wheel, it doesn't seem like it would cause pulling problems like on a car (where they can spin different speeds), I'd just have one rotor a bit warmer than the other. I'll likely do the safe thing and wait for the next pair to arrive, but curious.
May as well replace both at once. There will not be an appreciable difference doing one side then the other, plus the pads will seat rather quickly. I use 2000 grit wet/dry sandpaper on my pins to buff smooth any nicks on the shafts, then coat the shafts with silicon lub and let dry. I also lightly round the edges of the holes in the pads the pins go through so everything's smooth then put it all together...
I would hit the old pads w/ sandpaper and wait untill you have both sets. also hit rotors w/ sand paper as well.