The stone he put in its place looked almost exactly like Jon's stone, except that it wasn't. It was The Intermittent Stone.
It worked just like the normal stone, except that it would only grant every other desire. For example, if Jon were to say "I wish I was muscular and sexy," he would actually be wishing for two things within the same one sentence, but with The Intermittent Stone, only one of those two things would be granted, depending on what was granted before that wish.