My girl had the same problem. She also got little crusty bits on the tips of her ears. Vet wasn't quite sure what it was, and suggested that we start her on some fish oil and vitamin E and that has worked really well. The hair hasn't fully grown back, but it is getting there.
Nikon has had this on and off his whole life. I've had it swabbed, scraped, I had Dr. Dodds lab run a full thyroid panel on him....nothing, nada, he's super healthy, everything is normal/optimal. For him it's a circulation problem. No allergies, no autoimmune issue. Someone on another forum recently told me about a relatively inexpensive drug that helps with circulation that really helped their dog. I may look into this, but really it doesn't bother Nikon so it doesn't really bother me unless I want to bring him to a show.
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