Oh crap(!), I'm so sorry that the problems you mentioned have continued.
No advice, but I've looked at the EN ingredients in the past and they are a fair bit different than the I/D, even though the foods are designed for the same purpose.
He didn't have problems on the I/D from what you said, just stopped wanting to eat it, right? Do you think that was just pickiness or was his stomach starting to bother him? (As you know I'm a believer in I/D, Beth is on it and does so well, though she doesn't have IBD per se.)