I think it's the other way around d-jango. The show's final season was the last one. All the writers, crew, actors, etc. made plans to move onto their next projects. They taped and aired what they and the audience thought was the final episode. Then the network brought up a breach of contract or something and they all had to come back to make another season. The first episode of this season makes reference to that a couple times. Perhaps that would explain why almost every episode is missing a cast member of some sort. Maybe they had made other obligations at the time they thought Scrubs was wrapping up. I don't fully understand it, so don't take my word for it.