Board Thread:Questions and Answers/@comment-26343489-20160317221452/@comment-27701762-20160317233034

If you've earned EXP in the "current" run, then you have to start from the beginning. If you killed something, and then reset and started over from the beginning, then you've started a new run that is not impacted by your previous kills.

Basically, if Sans doesn't chastise you for killing anything, then you're in the clear.