Give page theme custom Permalink 404

Hello,

I want to change the perma link on a page theme basis.
This is what i’ve got so far in my functions.php:

//Change permalink to subject
function change_permalink_themebasis( $post ) {
    $template = get_post_meta( $post->ID, '_wp_page_template' ,true );
    if ( 'page-branches.php' == $template) {
        global $wp_rewrite;
     	$wp_rewrite->page_structure = $wp_rewrite->root . 'branches/%pagename%/';
    } elseif ( 'page-modules.php' == $template) {
	 	global $wp_rewrite;
     	$wp_rewrite->page_structure = $wp_rewrite->root . 'modules/%pagename%/';
	} else{
		global $wp_rewrite;
     	$wp_rewrite->page_structure = $wp_rewrite->root . '%pagename%/';
	}
}
add_action( 'add_meta_boxes_page', 'change_permalink_themebasis' );

It works but the problem is that the front page gives an 404.