I realize this doesn't help if we're just talking about the movie but, seeing as this post is recent and, coincidentally, I just started reading the Hannibal novel for the first time, I thought it interesting to mention:
I'm up to Chapter 10 (very early in the book) and it was just mentioned that Chilton 'disappeared'.
The exchange from Clarice to one of the former employees at the Baltimore State Hospital for the Criminally Insane:
and its clear that he died. Hannibal stalked him, killed him, and ate his face. Maybe even ate his face while he was alive. idk didn't read the book. but the phone call he had with clarice explains what happens, no need to show it or bring it up later.