Ok. I’ve recently discovered red dwarf. For various reasons the episodes I’ve watched haven’t all been from exactly the same source, which may have something to do with the problem.
Here’s my problem. Season two seems to completely lack continuity. Kryten appears in the first episode, doesn’t make an appearance again until the last episode. That struck me as odd, but not that strange, then I came to episode 6 - “inquisitor”. Kryten is back, as if he had been there all along, everything looks slightly different and Holly is suddenly female! Also the intro had changed. WTF is going on?
Did they remake red dwarf at some point? And if so, why the change in actor for holly - None of the original jokes would work with a female version.
IOW “Owww. My head hurts.” Please explain. 
Ahhh. Suddenly everything becomes clear. A mislabeled episode. It’s not the last episode of season 2 after all. Oops. Thanks Merrin.
Regardless, where is kryten throughout season 2 after his first appearance?
Kryten wasn’t originally planned as a regular character. They brought him back to the show in season 3 because, well, they wanted to make him a regular character, and, you’ll notice, they re-cast the role. Slow down the title crawl at the beginning of the first episode of the third season, they explain how they came across Kryten again and fixed him up (thus explaining why he’s physically “different”).
Riding around outer space on Lister’s motorbike thingy you see him driving off in at the end of his first appearence.
I guess he was supposed to be a one-off character, but they brought him back, explaining that they ‘recovered him after he smashed Lister’s bike into an asteroid’ or some such thing. It’s in the opening crawl from the beginning of Season 3, except it goes by in about 5 seconds so you can’t read it.
As for Holly, that’s explained in the same crawl. He fell in love with the female version of himself he ran into in that alternate direction (the one where Lister got himself pregnant with twins). He decided he liked her so much that he changed his face to match hers.
Hmmm. Haven’t used my .sig in a while. It seems appropriate here.