I am curious what made the internist think about lupus since it seems you consulted with him prior to the uveitis. This eye inflammation can be associated with many autoimmune disorders, and if your autoimmune blood tests were done over a year ago it would be worthwhile repeating them. Reflux and UTIs are extremely common. It’s the recurrent uveitis that makes one suspicious of an AI disease. I would make sure also that your stool tests included a fecal elastase level to check for exocrine pancreatic insufficiency,(EPI) which causes diarrhea. Chrohns and ulcerative colitis are 2 AI diseases that cause diarrhea and it’s worth getting tested again if the diarrhea is still a problem.
A consult with a rheumatologist would be helpful as they do the most thorough AI testing. I hope you get some answers soon!