Specific Page that convert Hyperlink to anchor in nav menu

First, throw away your custom walker.

Post URLs are called permalinks, and as with most things in WordPress, you can filter them! There is a filter called post_link that lets you modify the URL of the post before it’s returned in get_permalink(). We can use this, along with the posts slug, and the home_url function to get something similar to this:

function wpse183928_anchor_urls( $url, $post, $leavename ) {
    $url = home_url()."#".$post->post_name;
    return $url;
}
add_filter( 'post_link', 'wpse183928_anchor_urls', 10, 3 );

Secondly, your metabox and post meta you’re using for sections is the wrong way to do it. If you want to categorise things, you use a custom taxonomy, e.g. section category, you don’t repurpose pages and post meta to implement a custom taxonomy.

So register a custom taxonomy, call it sections, and assign it to pages. Now you can add ‘sections’ to your nav menu, WordPress will give you a user interface for free, your data will support import/export, and you’ll have an admin page dedicated to creating/editing/deleting sections made for you

Some helpful pieces of information:

A lot of people use a page template to implement a homepage. There’s no need, just use the home.php template, or index.php
When I say posts, I’m talking about a post of type post. Pages are posts too ( of type page ). Menu nav items are posts of type nav_menu_item, and images are referenced by post ID, where each image has an associated post of type attachment with post meta connected to it that stores EXIF data, descriptions, etc
WP_Query. People will suggest querying using query_posts. These people are not your friends, treat everything they say with suspicion, and never use query_posts
If you need to modify which posts WordPress retrieves in the main loop, don’t throw away the main query and create your own, use the pre_get_posts filter instead, it’s significantly faster

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