I recently had a biopsy that revealed Collagenous Colitis. I also have reflux. I tested negative for H-Pylori. However, I did show on a lower GI test an enormous amount of Dysbiotic/ overgrowth bacteria and very low good bacteria. Basically, SIBO (small intestinal bacterial overgrowth). I also have a high gluten intolerance based upon my Secretory IgA which my health practitioner believes allowed gut permeability causing the Colitis. So, perhaps this is something you may also have going on from what I hear you saying. Maybe you should get tested for SIBO.