Board Thread:Questions and Answers/@comment-27870742-20160226093936/@comment-27701762-20160226095735

Completing a Genocide run does...something...to your game files (semi-permanently). I suggest learning no more than that.

My recommendation would be to reset, do a Pacifist run, then do a Genocide run, then go back and do a Pacifist run. I like to think of it as the way it's meant to be experienced.