How to permanently destroy an instance?

I have 5 puzzle pieces in my game. They are instances of the same prefab. When the player walks over any of them, it gets destroyed and +1 is added to my puzzleCounter. However, when you are taken to the menu and then back to the game, the puzzles are there again (although the counter displays the number of puzzle pieces you have found).

How to permanently destroy an instance of a prefab, making sure it never spawns again until the game is restarted?

When loading a scene, all variables are destroyed. So, when you finish your scene and get to the menu everything is lost. But I guess your counter is a static variable, meaning it survives destruction.

In order to “remenber” what is destroyed, you could use this static variable to know how many pieces should be created on Load. But that draws one issue, if you play the game, finish the level, close the game and start again, your puzzle is not remembered.

Best way would be to look at PlayerPrefs. You could then save the different states of your game and next time you play or when you go back to the menu, it is all remembered.

PlayerPrefs is a little bit like having a database on your local computer.

When you finish the level you use:

PlayerPrefs.SetInt("RemainingPieces", 0); 

when you start the next time:

void Start(){
    int pieces = PlayerPrefs.GetInt("RemainingPieces");  
}