One way to know would be to go back on estrogen and see if the problem resolves. Assuming you don't want to do that, or it isn't safe to do so, you can continue to try dietary eliminations and probiotics, which may help to restore the natural bacteria that are supposed to populate the colon and help with healthy digestion.
My hunch is that the bowel issue is not related to the hormones. It is probably a coincidence.
See your doctor about any labs or imaging you might need to look for digestive problems. If nothing is found, healthy eating and probiotics may get you back on track.