Solar electric fence netting!That's what happened to me too! 6 foot fence around their enclosure and whatever it was was getting over. Foxes are notorious climbers. Locked them in the coop like you and then it figured out how to get under the fence for that part of the enclosure too! I tried trapping it (it tried digging under the trap), I tried hunting it, I tried having my boys pee, and I reinforced the section of fence it got under. I left my large black lab out in the back yard for a few days and any evidence of activity stopped completely immediately after that. Maybe you could borrow a dog? It will be back and soon.
They will not climb if they are zapped!