I've got a major Candida problem and my Endoscopy didn't show anything but a clean descending colon. I've flushed out lots of Candida with ACV Enemas so I know it's there somewhere. So this tells me my Candida is probably hanging out in the small intestine, ascending, and maybe transverse.
An Endoscopy only checks your descending colon. It doesn't go up into the Transverse or Ascending. You'll need to have a colonoscopy if you want to have the rest of your large intestine checked. I also don't think the holes created by the Candida would be big enough to see if there was no Candida attached to them.