I think what you did is correct, and the Path2D should be deleted when we shoot the enemy.
But if you did everything like in the lessons, the PathEnemy will be deleted when the timer hit 0, even if you shoot an enemy.
This is because when you shoot an enemy it will die, but the Path2D & PathFollow2D will still do its things, so the process won’t stop and eventually the progress_ratio will be at 0, and the queue_free() will be called for the path_enemy scene’s main node (so it will be completly deleted).
However if you set the PathFollow2D’s Loop On it wont be deleted, because the progress ratio will never reach 0. (I already did that mystake 
here: Disable the loop in PathFollow2D)