If I understand correctly, I think this is the same issue as what I need.
From what Kadar says it could be like this:
Website Area A
Menu Item 1
Menu Item 2
Menu Item 3
Menu Item 3a
Menu Item 3b
Menu Item 4
Website Area B
Menu Item 1
Menu Item 2
Menu Item 2a
Menu Item 2b
Menu Item 2c
Menu Item 3
Menu Item 4
Where depending which area the visitor is in, they will only see the menu items for that area. I suppose this might be done dynamically depend on which area the current page is... or possibly as 2 separate page skins, each showing one of the menus.
I'm not sure how the menus are setup to do this, and how the levels or 'IndicateChildren' actually works and relates to the page structure in DNN. What needs to be added to the Nav for it to work? And how is the page structure (like example above) actually setup to achieve this?
I've also noticed the links used in the default MinimalExtropy as follows:
<dnn:LINKS runat="server" ID="dnnLINKS" CssClass="links" Level="Root" Separator=" | " />
I'm unsure if that may lead to a solution, but I am guessing it doesn't include submenus and dropdowns.