I do not see why that is not possible, and probably even likely if the treatment is working as well as it should. What would be the point of treating if it had no effect on the problem?
It is possible it was not Crohn's, but since they really do not even have a definitive test to rule in or out Crohn's, other than a collection of symptoms, I do not know how they can be so sure of themselves.
I fully anticipate I will show nothing when the time comes to check. They have photos so they can't really deny that it was there to begin with.
So then the question is why are you having symptoms with no outward signs of disease. I would suspect a bacterial infection of one kind or another. Crohn's related or not.
Dan