I was thinking, the confusion is made because there's no clear feedback of what is being undone. It would be clearer if the interface displayed the context of the undone event.
For example, if you are in the event-editor and undo something from the layout-editor it should automatically change the view to the layout-editor so you can see what is being changed. In the same way when you undo an event it should select the undone event so the user can be aware of what is being changed.
I think the problems could be minimized this way.