I've only dealt with a muskrat once and it was soon after the pond was dug. The damage was incredible in a short period of time. Once we got our dog we never had an issue again. That may or may not be an option for you.

As for repairing damage, I happened to have some 1" size smooth rocks on hand and I filled the tunnels and holes with gravel (at the time I didn't know if the muskrat was around and would try to re-excavate the holes again or not). I hoped the rocks would make it less fun to try to dig in or back out of the holes.

If the muskrat are gone I imagine you could just try to backfill the holes that you can still access with dirt?