Like Still Standing, I am of the opinion that the diagnosis is just a label for bowel inflammation. Surgery isn't designed to cure autoimmune disease, which often manifests after surgery with new inflammation in new areas. So it's tricky to either say or prove that a misdiagnosis occurred. I was originally diagnosed with UC, had surgery, was 15 years later diagnosed with Crohn's in the ileum. The Crohn's that I have is much more controllable and less symptomatic than the UC pre-surgery, so if this was a "misdiagnosis" (which I don't think it was- just new inflammation in a new area due to autoimmune disorder), surgery was nevertheless a net positive for me.
For these reasons it's hard to draw any generally applicable conclusions about a change in diagnosis. In the final analysis it doesn't matter in a large number of cases, because the treatments are basically the same regardless of what you choose to call bowel inflammation caused by autoimmune disorder.
What is more important is where the inflammation actually is, whether it's in a new area and whether it's being adequately controlled. If it's not being controlled, doesn't matter what you call it. It's "uncontrolled inflammation."