I don't think they still LIVED up there, as they probably just thought of it as a hangout or something.
I remember the beginning of Season Six, Alvin was supposed to meet Brittany there for a date, it was probably their "special, secret place" or something.
The Chipmunk Adventure, however, was being written, and began production around 1984 or so, and back then on the show, not only were The Chipettes still living in their treehouse, but Miss Miller hadn't even been introduced yet, so production-wise, The Chipmunk Adventure was Miss Miller's first appearance, despite the movie premiering in 1987, like a whole year after The Chipettes moved in with her on the show.