My problem is with the Site Navigation Settings admin page:

If you delete a site or page node from the tree view there appears to be no way to recover them. I could create new nodes by hand, but then the menu system no longer dynamically changes to reflect updates to the structure of the sites and pages.
Does anyone know how to recover the original nodes, or even to reset completely?
You can’t recover any node that you have deleted in the admin interface – there’s no mechanism for that. You can set it back to automatic which will rebuild from the contents of the site.