You could restore the panes that are not part of the saved layout after the layout is loaded. To check whether a pane is loaded or not you could use the ElementLoaded event of the Docking control or to use the Panes property of the Docking control after the load of the layout is finished.
You could restore a pane that wasn't loaded in the layout by making sure it has no parent and add it into an existing PaneGroup that is already into the Docking control.
Hope this helps!
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