Bacteria Overgrowth

My 2 1/2 old son has had diarrhea for 29 days and vomitting for about 10 days. We went to the pediatrician a few times because it kept getting worse. Their diagnosis was Rotovirus. After bloodwork and stool samples, we found this to be negative. The chalked it up to a normal virus and dismissed it. After this continued for a bit and gotten much worse, we took him to the hospital where they gave him zofran to stop the symptoms and fluids. We were sent home after a few hours. He was ok for 8 hours and then the diarrhea and vomitting started again. I decided to seek treatment from a GI doctor because I was at a loss as to how to stop these horrible symptoms. My son had lost 3 pounds and wasnt getting any better. The GI doctor admitted our son into the hospital where he received Flagyl and Fluids for 3 days. All symptoms stopped while in the hospital. We got home and after 6 hours my son had diarrhea again and again in the AM. We went for an endoscopy which showed no celiac, chrons just reflux. The GI doctor said these symptoms were result of bacteria overgrowth and to continue meds and re-evaluate in 2 weeks. My ques is: should my son still have diarrhea daily? when will the good bacteria be restored? what caused the bacteria overgrowth? i hope someone can shed some light on this situation. My son hasnt been himself in over a month.
Thanks!