I was in a similar situation in that I was due an endoscopy & was taking Omeprazole. The doctor who was doing the procedure suggested not taking the Omeprazole for several days prior to it as it could affect the H pylori result. He didn't mention it affecting anything else. The doctor gets a good look at the oesophagus, stomach & duodenum & takes several biopsies so it suggests it is quite thorough.