There was another wish Jon could make to cancel some of the effects: "I wish that once I become a guy tomorrow morning, nobody else would remember that I had become a girl today."
Once the extra time expired, Jon was a girl in the hospital with her one year old daughter Jessie, but since Jon had not just given birth, there was a different reason he was there. She was just visiting Karyn, who still had just given birth.
Jon used a wish to make sure Karyn knew exactly what was going on, and after a while discussing the situation with her, went home.
The next morning, Jon woke up, fully male, to the sound of a crying one-year-old next to him. He recalled all the things that had happened the previous night, and how he had partly reversed the wishes. Only he and Karyn knew that there had been a whole series of wishes and reverse wishes involving the rock. Everyone else only knew the final result, which was at least easier to understand, and not as bad as it had been.
Sarah had, in some unknown way, wished Jon and Karyn pregnant at different times. Jon had had his baby, Jessie, a year ago and Karyn had had hers the previous night.
Unfortunately, that was still plenty to complicate Jon's life.
He got up, wished up a bottle to feed the baby, and looked around his room.
He happened to notice an issue of the school newspaper, which he had kept around for some reason. On the front page was an article: Pregnancy totem to be displayed again. The article went on to explain how a strange stone object, found in an archeological dig, had been brought to the school decades ago and been on display in the front hallway until someone tracked down a legend surrounding it. Anyone who touches it can use it to wish someone else pregnant; boys would become girls until the birth. A year ago, Sarah McMillan had touched it and wished Jon to be pregnant merely to try it out; she had been as surprised as everyone else to find it actually worked. Of course, as soon as that happened the device had been locked up. The school paper was a week old, but since then the object must have gone on display again. Obviously the security around it hadn't been very good and Sarah had managed to get to it again and wish Karyn pregnant.
So that's what the stone did in order to create a reality where all the wishes and fixes were true. Jon supposed that the totem must at least be locked up now. Or was it?