I have been doing some testing on the windows layouts and the containers. Basically I create new containers and save them to a new window layout. One of the is visible the other is not visible. Both are saved in the xml layout file that is created in the workspaces folder. But when I delete the containers, if I import the windows layout, only the visible one will be imported, the other will be missing.
This behaviour is different if I delete default rhino layouts, this ones are always restored, it doesn´t matter if they are visible or not. I attach a video for easier understanding.