When you talk to the vet next, you might want to ask if they peeked at Happy's intestines with the ultrasound. Maybe what they saw is "within normal limits" for an IBD dog so they didn't mention it. (I.e., maybe they saw stretched villi, dilated lacteals and such.) But I'd want to know one way or the other whether they looked and, if so, what they saw.
If they did look and didn't see any structural changes, maybe she doesn't really have IBD. Or maybe they're interpreting any changes they saw as consistent with a lengthy infection elsewhere.
Just a thought. It will make a difference as ongoing treatment and feeding is considered, so you should know whatever the vet knows.
Continued good thoughts and prayers!