I'm sorry to hear about the problem your son is having with thrush. I started on Advair last year, and my nurse practitioner told me before I ever went on it to rinse my mouth thoroughly after using it to prevent thrush. Don't know if that helps or not, but wanted to mention it.
I hate to hear that your son is having this problem. I can only imagine trying to get a handle on thrush in a young child.
I use Advair and have had thrush many times. Is your son rinsing well after using his inhaler? I rinse with Listerine whiteing pre-brush mouthwash, (half mouthwash and half water) it has helped considerably. However, if I eat something sweet like twizzlers or gummy bears, a weakness of mine, then it's necessary for me to use the rinse before and after using the inhaler.
I don't know if this will help you, but I hope so.
Also, I've never heard of someone having thrush for so long. I use the Nystatin liquid but I wonder about the Nystatin capsules. Perhaps he would have to be on them long term to get rid of the thrush. Also, after this length of time what are the chances that the fungus has gotten into the lungs or esophagus?
Please let me know how your son is doing.