Mary,
In general the navigation links are outside of the scope of s2Member control. However, you can do some tricky stuff that may work as you need. I won’t go into deep detail here because it would take too much, but I will outline a process for you that may work.
Add a plugin to your system called “Dynamic Widgets” by Qurl. This will allow you to restrict sidebar widgets to specific pages.
Go into WP Appearance->Menus and configure (a) your main menu navigation (name it ‘main’) without your special links, and then (b) a menu that has the special links (name it ‘special’) that you want to protect. Assign the ‘main’ menu to the Primary Menu, but don’t assign the ‘special’ menu to anything.
In the Appearance->Widgets panel, drag a ‘Custom Menu’ widget onto a sidebar, set your ‘special’ menu to be present there, then click on the Dynamic Widgets link and set it to appear only on the pages that you want your special menu to appear.
Now you have s2Member protecting your pages, Dynamic widgets restricting your widget to those pages, and the widget itself contains your protected menu.