I think the ttg numbers dropping on the gluten-free diet means something. If gluten was not causing a reaction the ttg shouldn't change right? How do his doctors explain that change?
I assume when you say he was scoped that you mean he had an endoscopy, not a colonscopy. Having both would be a good idea. But, an edndoscopy can only reach about 5 feet of the small intestine, and there are close to 22 feet in adults. So lots of unexplored territory there. Camera/capsule methods can see the whole intestine and take pictures along the way. But they can't get biopsy samples. So just because they saw little damage in the endoscopy does not mean there is not more damage further along.
I agree with the suggestions to remove dairy and soy from his diet. Both of them can cause damage to the gut. And recovery from soy and dairy can take several weeks or more, so don't give up on it right away. Another fairly common food intolerance is nightsahdes, potatoes, tomatoes, peppers and eggplant. Some of reacto corn or eggs too. Leaky gut can cause intolerances to any food out there.
Most chocolate has soy and dairy in it, so you might try carob on him instead. You can get carob powder in health food stores. I know dairy makes me bleed, so it can do that.
The article linked below could be the reason he isn't testing positive on celiac disease tests.
Non celiac wheat sensitivity article
No, he had an endoscopy and colonoscopy together. They didn't want to have to go back later and scope again if nothing showed up on the endoscopy.
Thanks for the link. Going to read it now...