Various elements of the episode seem to suggest Kobra Khan was not part of the original script. The heroes often refer to 'Evil-Lyn and Webstor' without mentioning Khan, Khan has little dialogue or action, and at the end he has been forgotten about altogether when Skeletor only punishes Evil-Lyn and Webstor. This would seem to suggest he was added in at the last moment, but the production deadline meant that some parts of the episode could not be revised to accommodate him.
Orko: Today we learned something about the importance of listening to other people.
Orko: Just a sec. Vokan's big mistake was listening to Evil-Lyn without asking He-Man for his side of the story.
Orko: Before we blame somebody for doing something, we should always find them and ask for his side of the story. That's important, because sometimes we're wrong about who's to blame.
Orko: Remember listen to what other people have to say. What is it Man-At-Arms?
Man-At-Arms: Dinner's ready.
Orko: What? You said I'm right?
Attact Trak: Yes. Noone can be wrong all the time...not even you. Odds are that you have to be right sometime...why not this time!
Orko: Great! Even when I'm right, I'm wrong. And the only reason I'm right is because I'm wrong, and if I'm wrong it's because he's right about me being wrong!