Uhmm I think you may have deleted your navigation (possibly in your header.php file?).
Are you using the menus? Maybe you can just add in <?php wp_nav_menu(); ?> somewhere in your header, then just rebuild from there.
I did delete something in the header menu, but even right after that it didn’t effect the links in any way. Only after I messed up with it afterwards then it suddenly disappeared.
And I do plan on using the menu for the site. Here’s an idea of what the website with look like once it’s done.
http://i60.tinypic.com/2qmgcv8.jpg