Board Thread:Questions and Answers/@comment-32948273-20160129174948/@comment-27280998-20160211215124

I think, at most, Flowey created some kind of small empty pocket dimension of a room to trap you in while he toyed with you rather than actually unmaking existence. He interferred with the player by closing the game, replacing their save in a new room, and changing the opening, but it doesn't really have to affect the rest of the world in Undertale.

He is very personally targetting and screwing with you because you are the only person in this world that he cannot predict, and up until that point he hasn't had enough power to thoroughly mess with you the way he wants to.