Sorry to hear she's having this, I wish the best for you and her.
I would see a diff specialist and see their take on it. It seems odd how they can't get a proper DX for her.
They did a lot of tests on her, something should show or know what's going on.
I see you mentioned they did a colonoscopy, but have they ever done a endoscopy, where they go down her mouth, to her stomach yet? They did that with me and didn't find it, but it can occur from the mouth right down to the butt. They found my crohn's in my small intestine by doing the colonoscopy.
Has she been tested for celiac disease, thats why originally they did the endoscopy for me.
I had D, gas and pain in my stomach.
Also, have you tried limiting foods that make her not well, like milk, beef, green veggies? A lot of people with crohn's can't handle certain foods. Let us know, remember we're here for ya! :)