You could set a global variable on Layout 1 as an indication that such-and-such sprites should be destroyed or created. When Layout 2 is loaded check the variable in Start of Layout and create or destroy them as then needed.
Thanks, I was hoping I was just missing something simple again.
On a related note, is it bad to set up more than one array?
I prefer to use smaller data sources, more localized. Like one array for the player, one for the enemies, and so on, instead of one large array.