Genesis filter genesis_skip_links_output to add the registerd menu 'foo-menu' to the array. See other gist https://gist.github.com/carasmo/a988e9b4126cdb9f28e6

add-to-functions.php

<?php
// don't include this


/** ====================================================================================

 * add skip links to new nav
 * filter 'genesis_skip_links_output' to add new 
 * https://gist.github.com/carasmo/a988e9b4126cdb9f28e6

==================================================================================== **/

function foo_nav_skip_links_output( $links ){

	$foolink = $links;	
	
	array_splice( $foolink, 3 );

	if ( has_nav_menu( 'foo-menu' ) ) {
	
		$foolink['foo-nav'] = __( 'Skip to Foo Nav', 'your-text-domain' );
		
	} 
	
	return array_merge( $foolink, $links );

}

add_filter( 'genesis_skip_links_output', 'foo_nav_skip_links_output' );