Yes, keep taking them, or switch to a liquid diet for a couple weeks. :)
HCL production is aided with lemon juice, good Sea Salt (salt deficiency is a prime suspect) and vitamin B6.
ulcer type bacteria is kept at bay by friendly microbes such as acidophilus and soil-based organisms, which also create B vitamins in the gut! so to have both a deficiency of stomach acids AND an ulcer really says loud and clear that you are deficient in friendly microbes.
Primal Defense is the best SBO supplement that I know of, and for live acidophilus it doesn't matter so much what brand as how fresh it is. Kefir is a good source because they have plenty of food sources and end up thriving, while capsules tend to starve them to death.