Here's what happened:
* The Stone was nearly destroyed: Voldemort tried to use it to regain his body but failed. The stone was left weakened and cracked.
* The Stone was taken away: Dumbledore decided it was too dangerous to leave the stone in the castle, even weakened. He removed it and destroyed it himself.
* The Stone was never found again: The stone was destroyed and its existence was not made public knowledge again.
So, Harry Potter did not find the stone after it was destroyed because it was never destroyed in the first place.