I have carbon wheels with the appropriate brake pads. During a race I flatted and quickly swapped wheels and finished the race. The wheel I used was aluminum, do I need new brake pads due to possible shards that will ruin my nice wheels or can I just clean them?
You can use them again, but you just need to clean them up. If there are any visible pieces in the pad, then remove those. After that, you just gently sand/file off the braking surface of the pad until you only have fresh rubber exposed.
You can go through the pads and try and pick out any metal shards, but are you sure you got them all? You just need one to damage the carbon brake track (e.g., a deeply embedded metal shard). Given the cost of the wheels, I think the more sensible option is to replace the pads.
This is unfortunately is part of the cost of racing.