[spoiler]Considering how the whole situation was completely botched during the Leviathans period, clearly no one knew how to deal with Chris/Quentin post 1897. So, it's never really surprised me that no definitive explanation for why Chris, Sabrina and Amy left town was ever given (though in reality we know that it was because Don Briscoe and Denise Nickerson were no longer available to appear on the show).
That being said, though, Sabrina was continually trying to persuade Chris that they did indeed have a future together. So, with that in mind, it also never really surprised me and it seems perfectly plausible that Sabrina and Chris would leave Collinsport to attempt some sort of new life - and, of course, that they would take Amy with them.[/spoiler]