Famotidine/ Green watery mucus poops/ Cow milk protein allergy?

My little girl is 6 months old. She’s using famotidine for her acid reflux from past couple of months and doing fine with milk intake and fussiness since then. We all got sick a month back with the virals. Little one started diarrhea along with cough, cold, fever and followed by an ear infection for which she had to use antibiotics. The diarrhea continued throughout the course of antibiotics and later as well. We are doing probiotics as suggested by the doctor and tested her poop for any stomach bugs /virus or blood in it but everything came back normal. She takes breast milk in bottle.Her stools are watery with mucus and color changing between green and yellow. We are doing rice, as suggested by her doctor to see if it helps to harden the poop. But no change yet. Now the gastroenterologist suggesting to take away dairy from my diet to check for Cow milk protein allergy. Any mamas with babies having acid reflux/ milk protein allergy, could you please shed some light. Is the chronic diarrhea because of allergy? Did the allergy developed because of acid reflux or the other way round??