This may already be someone’s fanfic, actually. I’d probably read it.
Someday, passage between the human and pony worlds will be much more common. At some point between then and now, a sort of intermediate step will be established, involving control over who may go through the portal, and how many at a time. Sunset and Twilight will act as guide between the two, giving basic information about the differences between pony and human bodies that will come in handy immediately, like changing whether or not horns and wings are present, and the change between being a quadruped and being a biped so ponies don’t spend their first few seconds as a human galloping off on all fours.
Lyra will be the first non-main pony to be allowed into the human world. She’ll be a bit miffed when she encounters Sunset, however, as what she remembers most vividly of Sunset is asking her if she’d like to have lunch with her and her friends and being rudely brushed off (compare Twilight, who was more apologetic about not attending the party for Moondancer). But Sunset will sincerely apologize, and Lyra will accept it easily.
The Bon Bons will be there on both sides to see their respective friends off, and meet the other version.
Pony Lyra will also come out clothed differently from Human Lyra, and Human Lyra will be wearing something upon emerging, which is relatively unusual for Pony Lyra, but not unheard of.