UPDATE!
Smaug brumated for almost 4 months. He seemed so droopy for the two weeks following, I decided to take him to the vet and just as Drache613 predicted, he had parasites. I am currently treating him, with Panacure and flagyl. He seems to be doing well at day 3 into his treatment. He is head bobbing and running around again.
The vet said that during brumation a reptile’s immune system goes down due to the lack of nutrition, allowing parasites and bacteria to grow unabated.