Board Thread:General Discussion/@comment-27907368-20160506131212/@comment-27620479-20160519093241

PancryPancreas5 wrote: I doubt Flowey ever regains control... I mean, when we don't play the game for a long time and then decide to play it, we don't see Flowey taking over it, haha... In case you have forgotten it, you load a save. Any progress you make after your last save is lost when you quit or reset.

So, Flowey can take over while Frisk is away, and Frisk doesn't make saves after leaving the underworld. It is either Flowey taking over, or a time loop.