A lot of rabbits contract mites on and around their ears. These are parasites that burrow into their skin. They can cause itching, flaking and sometimes loss of fur. If this is what your rabbit has, it has to be treated until all mites are gone. Make sure the cage is cleaned with bleach and hosed off before he goes back in. A vet can give him a prescrition for Ivomec, which is used to get rid of all types of parasites in rabbits. Some people use flea powder made for cats (dog products will hurt your rabbit).
I hope that this helps you out some!
Moe
I hope that this helps you out some!
Moe