function bv_procedure_parent_slug($url, $post) {
    if(get_post_type($post) == 'procedure' && get_post_meta($post->ID, 'procedure_parent', true)) {
        $procedure_parent = get_post(get_post_meta($post->ID, 'procedure_parent', true))->post_name;
        if($procedure_parent) {
            $url = str_replace('procedure', $procedure_parent, $url);
        }
    }
    return $url;
}
add_filter('post_type_link', 'bv_procedure_parent_slug', 1, 3);

function my_custom_rewrite() {
    add_permastruct('procedure', '/%parent%/', false);
}
add_action('init', 'my_custom_rewrite');