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Has your son had any fevers? Has he been comting?
During this workup, did he have a colonoscopy where they take a camera and look at his intestines?
It sounds like he might benefit from a colonscopy but if he continues to feel bad, you should probably take him to see your doctor. Things to make you get an appointment even sooner or go to the ER include things like vomiting, not eating, fevers, not having a bowel movement for more than a day or so more than usual or not being able to pass gas, or just generally feeling really sick.