The stone he put in its place looked nearly the same as Jon's stone, but it wasn't. It was The Isolated Obvious Stone, which worked just like the original stone, except that anyone who was directly affected by a wish would notice the changes in reality, not just the people who heard the wish.
So, for example, if Jon wished that Sarah McMillan was the most unpopular person in school, then Sarah would still remember the previous reality, but all of her friends wouldn't, even though Sarah's loss of friends would have been caused by the wish.
