When Lister (Craig Charles) is talking about breaking down the ship's internal doors, he accidentally blows out the lighter that he took out of his pocket.
With the white-hole plugged and its influence eradicated the time-line resets to before they encountered it: Holly returns to her normal self and Kryten states that they will have no memory of the events. This means that there is nothing to stop Kryten from enacting his plan to fix Holly again, but this time there would be no white-hole to save them.