Kelcee lost her hair from flea treatment too, but only where I applied it, behind her neck. I stopped using it after that.
The vet may do blood work and that should tell you what's going on in his system, if anything. They can also do allergy test. This is the first time this has ever happend to him? Poor boy. Good luck. I'm sure they can fix him right back to his hairy little self in no time