What difference would that make to the nanobots? Given nanobots re-arrange existing molecules, at first I thought they re-created the crew from the piles of dust we saw in The End. That would explain why Lister isn't there, but Kochanski should be. If we include the deleted scene from The End where Lister fires everyone's dust into space, then it still doesn't make sense, because while he does jettison Kochanski's ashes, he also jettisons Rimmer's and three other people's and presumably everyone's. We can assume that deleted scene did happen because the piles of dust were gone by Future Echoes.