After the stone glowed for a second time, Jon's eyes went wide with shock. His grandfather's wish was:
I wish Jennifer was born as a boy named Jon.
Jon didn't know how to react. He was just finding out that he was supposed to be a girl. And now that life that he never knew was completely wiped from existence. Jon knew that his grandfather favored boys over girls when it came to children, but he never thought he'd do something like this.
Now since Jon knew the truth, he began to wonder what his life was like. He would never be able to become a girl, of course, since that would be a contradiction to his grandfather's wish, but maybe he could at least wish to have the memories of that life. He just didn't think it was right for that reality to be totally forgotten.