Hi Jamie. This happened to me also. I thought I had UC, diagnosed via colonoscopy and biopsies. I had no reason to doubt it really. Then my next colonoscopy, as soon as the doc was done scoping me, he said that he was 99% positive that I was misdiagnosed and it was Crohn's. The biopsies confirmed it this time as well.
I believe that it's just not possible to tell the difference sometimes. I was so severely ill by the time I had my first scope that my colon had the appearance of pancolitis. Inflammation everywhere. The next time though, my colon had the "skipped patches" of inflammation that are seen with Crohn's. And, the "granulomas" that were present in my biopsies to confirm crohn's don't show up every time I am scoped. My third scope they were once again nowhere to be found. I also had the Prometheus test done, confirming CD. However, there are many who claim that the test is not all that effective. I am confident in my CD diagnosis, but it took me some time to feel that way.
I would say that since you have a history of fistulas, and your disease appears to be following that "skipped" pattern, that your doctor has good basis for what he is telling you.
I know that it is difficult to accept this kind of change in diagnosis. Feel free to Email me if you would like. I went through it all myself, not so long ago.