At the beginning of the Back to Earth special, we see Lister reading to a memorial to Kochanski, with the implication being that she is dead.
Later in the special, the kids Lister talks to on the bus talk about the events of "Series 9", which was never actually written, shot, or aired. They tell him that Kryten lied about Kochanski being sucked out of an airlock. The truth, according to the kids, is that she was tired of watching Lister wasting his life drinking and went off on her own in Blue Midget. Kryten told Lister she had died in order to spare his feelings (or perhaps because he was jealous of Lister's feelings for Kochanski).
At the end of the Back To Earth specials, Lister resists the hallucinated Kochanski, saying that he knows that the real her is out there somewhere and that he intends to find her.