I'm not sure how to upload a demo of this, so I'll do my best to explain.
1) Create a new project
2) Add a sprite and an array to the layout
3) Duplicate the layout.
If you now compare the two layout XML files you will notice that the sprite was copied fine, but the array is missing in the '<nonworld-instances>' section.
Side bug: If you have two pre-existing layouts and you add an array to your game, it is only added to the layout tab you have open (so you can have both layers open, but only the active one will get the array).
If I manually copy the array XML to my new layer everything works fine.