The stone he put in its place looked exactly like Jon's stone, except that it wasn't. It was the Barter Stone. It worked just like the normal stone, except that when someone makes a wish with it, something from his or her life gets erased from existence, just as if the wisher is trading something for the wish. Anything that is removed from existence with this stone cannot be wished back, so the removal is permanent.
The value of the wish is determined by the stone. The bigger the wish, the higher the price. The smaller the wish, the more trivial the price.
Only the wisher and those who hear the wish will notice the absence of whatever has been removed from the wisher's life. To everyone else, it will seem as if reality had always been that way.