When you are instance()
-ing and add_child()
-ing your enemies also:
var new_enemy = enemy_scene.instance()
self.add_child(new_enemy)
new_enemy.add_to_group("enemies")
Then when you pick up that item you can:
for enemy in get_tree().get_nodes_in_group("enemies"):
enemy.die()
alternatively:
get_tree().call_group("enemies", "die")
Replace die
with whatever function you use to kill your enemies normally.