I wouldn't change back and forth.
Here's a similar story. At the beginning of Sept. I took in an adult rescue (20"
, he weighed 269 and was injured. He was very afraid of people and bit me twice the first week.
All my hospital enclosures are glass terrariums. He spent 3 months in one on shelf liner and is healed and 450 now. He calmed down and became no problem to handle. A few weeks ago I moved him into a melamine enclosure with sliding doors. It is about the same size 4' x 2.5'.
Now he seems scared when I open the doors or reach in. This is a change. His eating is normal but of course he is still underweight. I think maybe they get used to seeing in every direction and then feel restricted with only a forward view. You also now just appear in his line of sight when he used to see you coming. I'd stay the course with the enclosure he is in. But, in my opinion a 36" x 18" enclosure is really to small for an adult dragon. He really should be in one at least 2' x 4'.
As far as brumation, put a hide on the cool side and see if he uses it. It seems awfully late in the season for a dragon to start brumation.
Since your only symptom is that he's not eating much, I recommend you get a weight scale. Sometimes they just eat less. If they eat less or little and don't lose weight then I wouldn't be concerned about it. If he is losing weight then a vet visit is likely in order.

