I've been dealing with having my Crohn's dx questioned also. I was dx'ed about 5 yrs ago by capsule endoscopy, when everything else had come back okay (except Promethius said I had UC). Crohn's was in the TI, which is why it never showed up on colonoscopies. Anyway, Remicade put me in remission and I've stayed in remission with Cimzia and Humira (have switched back and forth a few times after having allergic reactions to Remicade).
Fast forward to now and the "Crohn's related arthritis" has gotten so bad and we have exhausted all options except for stopping Humira and trying Enbrel or another biological just for RA. GI first said no because my "Crohn's has proven very difficult to treat in the past." Asked again 6 months later and was told he would do some tests to find out if I "even have Crohn's" or if it's "just IBS." Um, what? So, after being on dangerous meds for 5 years, he is questioning the dx now that we have to make some big decisions about my treatment. I was so confused. Anyway, colonoscopy came back suspicious for Crohn's but then the biopsy was normal. Waiting on the results of my capsule endoscopy from last week. I don't think I will believe him if he says I never had Crohn's, because the Crohn's meds made me so much better and because another GI thougth he saw Crohn's on the pillcam. But, it would give me another option for the arthritis treatment.
So, I completely understand feeling confused and lost because Crohn's has become part of who you are. It would be great not to have it now, but it would take some time to adjust to who you think of yourself as being.