It was found by Karyn. Considering that she was right there to see Jon drop it.
"Jon!" she yelled. "Come back here!"
"I think we've done enough using that stone," he replied.
"Wait, something's wrong!"
Jon walked back to the restroom, slowly, after pulling up his pants. The absence of a penis was pretty much not visible. "Karyn... what do you mean?"
"I mean," said Karyn, "that you can't reverse wishes. How did that wish make me not your penis? That's a reversal."
"Why not ask the stone?" wondered Jon.
They did, and they found the answer. Just a few days before Jon's grandfather willed Jon the stone, he was going to make a dangerous wish and had made a failsafe--he wished that the next wish that the owner of the stone considered really bad, could be reversed. He never needed to use the failsafe, and Jon ended up getting it.
"So it's okay," said Karyn. "We just need to get rid of your wrong parts. I wish..."