I had this issue with my horse last year (not year before, not this year). She shed away lots of hair and ended up with bold spots here and there (kinda looking like yours but bigger). It happened after she was with no shelter for month under the rain (the new gelding kicked out all horses from there and that was main reason I moved both my mares away from the place). My guess was rainrots, but I never talked to vet (it didn't look bad - just bold). After I moved her to my place with shelter and all she grow the hair back in 1.5 months. I didn't use anything on skin, just let it go naturally.