The only reference in the PHP code I can find to #secondary seems to exist in the header.php file,nested in the nav bar Div:
<nav id="access" role="navigation">
<h3 class="assistive-text"><?php _e( 'Main menu', 'twentyeleven' ); ?></h3>
<?php /* Allow screen readers / text browsers to skip the navigation menu and get right to the good stuff. */ ?>
<div class="skip-link"><a class="assistive-text" href="#content" title="<?php esc_attr_e( 'Skip to primary content', 'twentyeleven' ); ?>"><?php _e( 'Skip to primary content', 'twentyeleven' ); ?></a></div>
<div class="skip-link"><a class="assistive-text" href="#secondary" title="<?php esc_attr_e( 'Skip to secondary content', 'twentyeleven' ); ?>"><?php _e( 'Skip to secondary content', 'twentyeleven' ); ?></a></div>
<?php /* Our navigation menu. If one isn't filled out, wp_nav_menu falls back to wp_page_menu. The menu assiged to the primary position is the one used. If none is assigned, the menu with the lowest ID is used. */ ?>
<?php wp_nav_menu( array( 'theme_location' => 'primary' ) ); ?>
</nav><!-- #access -->
</header><!-- #branding -->
<div id="main">
Moving this div doesn’t seem to have any effect however which seems very odd.