As much as I'd love to have Skeeter Retconned in any Muppet project, it's painfully clear that even under Henson, The Muppets and Muppet babies were designed to be 2 different franchise that were never meant to cross into each other. With the exception of the Muppet Babies storybook and cartoon videos and the software hosted by adult Kermit, and that one scene in Muppet Family Christmas (which raises questions). I don't think they ever wanted, or planned on incorporating Skeeter at all. I'm surprised they even address her in fan terms as lost off in some adventure. It would be so easy to address her as a cartoon only character like every single cartoon ever made based on a movie (still ticked they didn't bother putting XR, Booster, and or Mira Nova in the background of Toy Story 3).
It would be great if they got the message, though. But I'm still thinking they want Muppets and Muppet Babies miles apart from each other. That may be a bigger factor for Muppet Babies not being on DVD than copyright reasons.