In your RestartGameButton class just return after this line

GameManager.instance.RestartGame();

because after this line your code continues to this line

SceneLoader.LoadScene(2);

and this line is loading scene in index 2 in single mode which will remove all loaded scenes

But if you want to load the load scene on index 2 then you have to update your scene loader to hold a list of loaded scenes and unload loaded scenes first and then load new scenes and while doing this just exclude your PersistentScene scene

On top of this I would recommend you to watch this tutorial