I haven't experienced it, but is your horse outside in the sun a lot? When I was googling the problem, I found this about about increased sunlight exposure and melatonin treatments as a possible treatment that is getting good results.
"Some veterinarians recommend melatonin as a treatment for seasonal alopecia. Melatonin is a naturally-occurring biochemical used by the body to regulate circadian rhythms. Melatonin can shorten the hair loss episode and prevent recurrence, according to the District of Columbia Academy of Veterinary Medicine, which reports a 50 to 75 percent positive response rate to melatonin treatment. Melatonin, in oral form or injections, is given until your animal begins to grow healthy hair. Melatonin also is used to prevent or treat future occurrences of the condition. Some veterinarians prescribe oral melatonin and increased sunlight exposure to treat seasonal alopecia. Animals receiving treatment have varying degrees of success at growing new hair."
DVM360, an online veterinary magazine, cites lack of exposure to sunlight as the cause
