Instantiate a prefab just one time

Assuming you want it to work between game sessions, then you need to persist the fact that the player has picked it up. There are several ways, depending on the type of game, and how many you need to save. A simple solution would be to use PlayerPrefs. When the scene loads, you just need a component that does something like:

void Start()
{
  if( PlayerPrefs.GetInt("ItemPickedUp") == 0 )
  {
    // instantiate it here
  }
}

And when they pick it up, in whatever "Pickup" function you have, add:

// store that they picked it up so we don't respawn it
PlayerPrefs.SetInt("ItemPickedUp", 1 );