What is your humidity, and what are you using to heat?
I have had this happen before and it usually resolves itself. My poor boa had been having a lot of RI issues (unrelated) and going to the vet a ton, and he had tons of shots and injections, and would constantly shed his skin. The last time he shed, it was awful - he has NEVER had a bad shed before, so I don't know what caused it, but now he has these patches on him. Of course, he has resumed a normal shedding cycle and is eating again, so he has not shed yet, but I assume it will resolve itself in the next shed or two, which is what I assume will happen with your guy.