The stone he put in its place looked exactly like Jon's stone, except that it wasn't. It was the Materialism Stone. It worked just like the normal stone, except that it could only grant wishes for physical objects (things you can touch, but nothing that's alive). There's one catch, though. The objects wished for by use of this stone are not conjured up, but instead they already exist. The stone basically steals them from other places, within the wishing range of the stone.
Also, reality does not change when this stone is used.