I don't think that's how Alvy's story ends, considering that Therium's route is also undone by time being wound back to the "true route" crossroads at emo horse's office.
There's some weird meta narrative going on where the narration is aware those other timelines occurred even if they were undone. Maybe whatever magical conspiracy is being weaved needs those events to have occurred, for reasons that will be revealed later.
Have faith brother, I'm positive we'll be seeing more of Alvy
Edit: As in, as a character, but I imagine not with him as a focus, in the same way we keep seeing Therium outside of his dedicated route popping up, he is still going to be there in the greater story is what I'm trying to say. That's my theory anyway