Obviously your dog has its own issues and I have no insight on acid reflux other than personally, I felt the drugs caused more problems than they fixed and I went to managing the foods I ate and the time I ate them.
My dog has some issues with getting a really firm stool but part of it to me is the volume of food he eats..... but no other issues. I have given kefir but it did not resolve that.
My veterinarian gave me this which you can order online at a better price and it seems to work real well and has excellent reviews everywhere. Picked up a stool and, oh my, it had no real odor. Between that and the prozyme I give all seems pretty good.
Proviable DC for Dogs