Board Thread:Questions and Answers/@comment-33019241-20170210032017/@comment-27701762-20170210032422

I'm not sure what you mean by "different save file." The game only keeps one save file at a time regardless, and in a sense every time you perform a True Reset (i.e. completing the True Pacifist or Genocide route), the game wipes the various files associated with the previous run/runs.

Completing a Genocide route sets a permanent flag elsewhere in the game's code, which is not associated with the "save file" in any way. So using "a different save file" wouldn't mean or accomplish anything. You would need to remove the flag from the game's code (as described in the "Consequence Avoidance" section on the Genocide Route page), or erase the game files completely and redownload the game.