I got it from Cipro when I still had my colon once and think I had a recurrence the other time(s). I don't think the PPI caused it with my j-pouch but who knows for sure. I waited too long to seek help when I found out I had a bad case of cuffitis and pouchitis or IPS and c.diff. The reason why I don't know is my surgeon did a straight scope with no biopsies and started treatment for the cuffitis with anucort. I went to my GI a month later and he treated me with canasa after discussing the visual only scope with my surgeon. When I was still very ill he did a proper pouch scope with biopsies and it was a mess with cuffitis and he took a stool sample, knowing my c.diff history..... This was several months into treating my pouch with anucort or canasa. It took several rounds of Flagyl to get rid of the c.diff and it recurred several times. I started the specific probiotic I discussed above and have not had it since. I've been on the PPI the entire time.
I've had several Endoscopies and besides having my hiatal hernia and GERD my GI has had to dilate my esophagus twice. I don't know how this factors into the PPI use but I've tried weaning off of it before and I get sick.
We have enough problems with our j-pouches as it is and I can understand your concerns. Maybe you can discuss them with your doctor and s/he can figure out a different route to take or figure out how to take a smaller dose to find the minimum amount you need. I use to be on a stronger PPI. I have not had any problems since starting the probiotic, is that why, I doubt it but it could be. I would have been taking it from the beginning if I realized there was a specific one to fight c.diff. I would have been taking it back when I had my colon. I take VSL#3DS too, I'm all for prevention. I take B12 as well and run on the high end of normal when my blood is tested.
There are long term consequences of not treating acid reflux so it could be damned if you don't too