Edit: Actually this method won't work because I don't think you can save instance variables.
If I understand correctly, you want to destoy the enemies that were already killed prior to saving right?
Just create a new instant variable on the enemies object (or family), name it someting like "death", and when you kill an enemy, change that variable to 1.
Then make a new action on layout start to destroy the enemies that have that variable to 1.