I bought a bicycle with carbon wheels, and for training I purchased an aluminum wheelset. I have SwissStop brake pads. Can I use them with aluminum wheels? I don't care much if these pads wear out quickly (I am going to buy new pads for races) but I worry more about braking performance.
In short yes you can, carbon brake pads will stop you but you shouldn't. Firstly the brake pads will not be as effective on the alu rims. Secondly the change between alu and carbon rims could be risky to your carbon wheels, a tiny fragment of alu from the training wheels could damage your carbon rims (source: Swiss stop website).
So to answer your question yes you can, but is it worth it for the 2 minutes it would take to switch between the correct brake pads when you change wheels? Personally, I think no but it is down to you.