Board Thread:General Discussion/@comment-5413572-20160521063300/@comment-28394344-20160527105303

Mabian wrote: There's the sort of quantum uncertainty problem at play here: we observe in the credits sequence time moving forward, and yet we also return to the game just before that same sequence. Don't forget that Flowey knows about your SAVEs and loads, and unless he somehow can't tell if you reloaded your SAVE or not after destroying the barrier, he would know what the human did after everyone left on the surface anyway. Kind of.

Flowey could not actually pay attention, though, or the human may still be Frisk, but with their mindset being entirely replaced to Chara's, so he would still differ them both, or something else...

I don't think there is a serious in-universe explanation. Pretty much.