Many in the 'GERD community' seem convinced that Betaine HCl (the supplement that improves stomach acidity and digestive efficiency) shouldn't be taken when using PPIs because they have opposite effects. However, this scientific paper - http://pubs.acs.org/doi/abs/10.1021/mp4003738
...which is *typically* free to those on a major college/university internet network (or is otherwise $40 to access), seems to show that the a PPI and Betaine HCl could be effective when used together. Without having to pay, the two most important figures are viewable for free in the link I provided.
To summarize the paper, the use of rabeprazole induced a state of hypochlorhydria in patients (where the stomach pH doesn't get very acidic, which can inhibit digestion and vitamin absorption), which is expected when using a PPI. But even while on rabeprazole, after taking 1500 mg of Betaine HCl, the stomach contents become much more acidic even after a few minutes of taking the digestive supplement. This effect seems to last for ~1 hour before returning to the hypochlorhydria condition induced by the PPI (probably after the stomach contents empty).
In other words, it seems like you could use the PPI to increase stomach pH (make it less acidic) throughout most of the day, and then use Betaine HCl when desired (like after a meal) to induce a short term (~1 hour long) instance where the food is being properly digested and nutrients are being properly absorbed. Beyond this article, there is not a ton of research available on the combined usage of Betaine HCl and anti-reflux medication, and mostly we just rely on the experiences from others in the community (like on this forum).
Hope this helped.
Post Edited (EJohn) : 6/25/2017 2:47:38 AM (GMT-6)