What do people mean when the Genocide Run scars their game file? I am thinking of starting one, but I don't want it to get ruined.
Yes, the player's SAVE file is deleted, and the game is now permanently altered.
When you complete a full genocide run in Undertale, any pacifist game plays afterwards will be affected. This being in the ending. The change comes in the last moment of the ending. A small, but significant change if you want your proper happy end. You can close the game and reset your playthrough as late as the final decision you are given at the end of the Genocide run and you'll be fine, if you don't want to hinder future pacifist runs. There'll also be slight dialogue changes.
Upon relaunching the game after Chara destroyed the world, the game now only has a black screen with the sound of howling wind. The inputs do nothing here. There are no menus. No buttons, nothing. The world is no more. After waiting approximately 10 minutes on this screen, Chara notes the player's return to the game. They remind the player that they are the one responsible for the world's destruction, observe that the player cannot accept that they caused it to happen, and then coldly remarks that they think they are above consequences.
If the player affirms by selecting 'YES,' Chara will simply say, "Exactly." If the player selects 'NO,' Chara will ask the player, "Then what are you looking for?"
No matter which option is chosen, Chara then states that a compromise could still be made. They state that the player has something that they desire, and offer to restore the world if the player surrenders it. If the player says "YES," Chara reveals what they want from the player: their SOUL. If the player agrees again, Chara states that the deal has been made, and the game closes once again but appears to boot up normally the next time it is opened. The player's SAVE file is deleted, and the game is now permanently altered. From that point onwards, any future playthroughs of the True Pacifist Route and the Genocide Route become dubbed by fans the "Soulless True Pacifist" and "Soulless Genocide" Route. Unusually, this does not affect the Neutral Route endings at all.
Read about all the details of a Genocide Run on the Wiki.