Board Thread:Questions and Answers/@comment-33019241-20170210032017/@comment-25958552-20170210075946

There is only one save file in the entire thing. You can't change something. Whenever you multiple end the game and reset your file, things change there and remain there. Like in true pacifist run, chara's face would appear in the bed and a photo with everyone marked "X".

As Mabian said, it sets a permanent flag in the game's code. Toby Fox didn't manage multiple saving files. If you don't want wierd consequences to happen from the genocide route, exactly, search the game's code for the flag or delete the game with the files.