They found out.

It was your 15th Reset. By now, you were fully aware of them, and Flowey wasn’t even trying to help you anymore. You made friends with everyone again, went through the Steamworks with Ceroba, before yourself an actual gun instead of a toy, and defeated Ceroba in battle after she tried to take your soul. However, this route was different. They refused to take your soul and complete the True Pacifist Route like it was supposed to be. Thus, you stayed with them in the underground, in the Wild East. However, due to Flowey’s interference, he was able t make everyone aware of the past runs. Including 3 specific ones… your Genocide Routes. You didn’t know until your friends confronted you about it

Martlet: …why? Tell us why. I want an answer.

Starlo: …so you’ve been lying to us? All those friendships and all that progress just for you to always reset it all, huh? Some deputy you are…

Ceroba: …Clover. This isn’t a joke. We want answers. Now.