I get the feeling that was a miscommunication that was quickly cleared up, yet Roger having his brand of humor, willfully just kept the gag going until the final issue of the arc. I don't see why it was an issue even with the character usage. Roger made some cryptic remarks about how Statler and Waldorf as the fates were thrown in to make it ambiguous that this was happening or not. I mean, even if the Muppets had a canon, I doubt the comic book was going to be acknowledged anyway. Adult Skeeter is as much a Muppet character as Kismet the Toad, Peg Leg Wilson, and Clint Wacky were. As in, they only exist in comic form.If you're referring to the trouble they went through to have her be named in The Muppet Show Comic Book, that was really Roger Langridge being unsure whether Disney would approve of Muppet Babies in the comic book series. But he eventually did get approval of having her name be mentioned.
Skeeter's odd lack of usage has been a thing since the Henson days. They never made her a real character outside of the show, and I tend to think that Disney's Muppet wing wanted to keep that going. That said, if we're asking where Skeeter is in all this, the more apt question is, where is Scooter in all this? The cast list, minus the new sheep character, is basically the main five cast members (read marketable). No Rowlf either. And I'd tend to hope that if this does get made, we'll still see Rowlf and Scooter and hopefully other baby/toddler versions of the Muppets, even if they're occasional recurring characters.