As CT wrote, the biopsies are unlikely to be informative. It’s worth trying to get the inflammation under control, but the fact that you feel good is much more important. Like you I’ve been on Cipro and Flagyl for a long time; I recognize that this combination may fail at some point (later better than sooner), and I’d have to find another treatment (such as a biologic). That’s true regardless of the underlying diagnosis. Ulcers in the pouch aren’t generally evidence of Crohn’s, anyway. I don’t think you’ll lose your pouch from asymptomatic ulceration.