When Jon made his original wish, he had said he could use the phrase "you can have it back" to reverse a swap made with the last person. So he could indeed reverse the swaps in any order as long as they were on the same person.
There were two changes to reverse, the breasts and the vagina. Jon said "you can have it back" and reversed one of them.
But then came an idea. Jon reversed the other change--using an index finger swap to swap the parts again. Now, he and Karyn were completely back to normal. But because he used an index finger swap, Karyn didn't know she was back to normal. She still thought she was swapped, and in fact she still thought her perfectly normal body was one she wasn't supposed to have.
Jon walked away, grinning.
"Hey, come back here!" said Karyn. "Are you going to leave me with...."