Custom Post Type Taxonomy - Permalinks generating, but posts not found

Question

I have a custom post type documenting Treatments available from a clinic. This sits on the Cosmetics part of the website (site.com/cosmetics/).

Filters have managed to translate \%type\ for permalinks. This is the structure I'm after: site.com/cosmetics/treatments

site.com/cosmetics/treatments/[type]/

site.com/cosmetics/treatments/[type]/[treatment]

I've already tried to follow many of he answers on here. Any ideas or obvious flaws in my code? I've been flushing the permalinks each time already.

site.com/cosmetics/treatments/[type] is working fine. Treatment pages themselves link to the following from the admin panel: site.com/[type]/[treatment] This is a 404 error.

UPDATE

I've rearranged some of the code, so I've changed the code on here to reflect that. The problem remains unchanged.

Plugin Code:

    class NSCTreatments {

        /**
         * Constructor for taxonomy and post type initialisation
         */
        function __construct(){
            add_action( 'init', array( $this, 'register_custom_taxonomies') ); // this MUST go first
            add_action( 'init', array( $this, 'register_custom_post_type' ) );

            add_filter('post_link', 'treatment_permalink', 10, 3);
            add_filter('post_type_link', 'treatment_permalink', 10, 3);

            function treatment_permalink($permalink, $post_id, $leavename) {
                if (strpos($permalink, '%type%') === FALSE) return $permalink;

                // Get post
                $post = get_post($post_id);
                if (!$post) return $permalink;

                // Get taxonomy terms
                $terms = wp_get_object_terms($post->ID, 'treatment-type');
                if (!is_wp_error($terms) && !empty($terms) && is_object($terms[0])) $taxonomy_slug = $terms[0]->slug;
                else $taxonomy_slug = 'no-type';

                return str_replace('%type%', $taxonomy_slug, $permalink);
            }

        }

        function  register_custom_taxonomies (){

        $labels = array(
            'name'              => _x( 'Treatment Types', 'taxonomy general name' ),
            'singular_name'     => _x( 'Treatment Type', 'taxonomy singular name' ),
            'search_items'      => __( 'Search Treatment Types' ),
            'all_items'         => __( 'All Treatment Types' ),
            'parent_item'       => __( 'Parent Treatment Types' ),
            'parent_item_colon' => __( 'Parent Treatment Types:' ),
            'edit_item'         => __( 'Edit Treatment Type' ),
            'update_item'       => __( 'Update Treatment Type' ),
            'add_new_item'      => __( 'Add New Treatment Type' ),
            'new_item_name'     => __( 'New Treatment Type Name' ),
            'menu_name'         => __( 'Treatment Type' ),
        );

        $args = array(
            'hierarchical'      => false,
            'labels'            => $labels,
            'show_ui'           => true,
            'show_admin_column' => false,
            'query_var'         => true,
            'rewrite'           => array( 'slug' => 'cosmetics/treatments', 'with_front' => false ),
        );

        register_taxonomy( 'treatment-type', array( 'treatment' ), $args );
    }

        /**
         * Registers a Custom Post Type called Treatment
         */
        function register_custom_post_type() {
            register_post_type( 'treatment', array(
                'labels' => array(
                    'name'               => _x( 'Treatments', 'post type general name', 'nsc-treatments' ),
                    'singular_name'      => _x( 'Treatment', 'post type singular name', 'nsc-treatments' ),
                    'menu_name'          => _x( 'Treatments', 'admin menu', 'nsc-treatments' ),
                    'name_admin_bar'     => _x( 'Treatment', 'add new on admin bar', 'nsc-treatments' ),
                    'add_new'            => _x( 'Add New', 'treatment', 'nsc-treatments' ),
                    'add_new_item'       => __( 'Add New Treatment', 'nsc-treatments' ),
                    'new_item'           => __( 'New Treatment', 'nsc-treatments' ),
                    'edit_item'          => __( 'Edit Treatment', 'nsc-treatments' ),
                    'view_item'          => __( 'View Treatment', 'nsc-treatments' ),
                    'all_items'          => __( 'All Treatments', 'nsc-treatments' ),
                    'search_items'       => __( 'Search Treatments', 'nsc-treatments' ),
                    'parent_item_colon'  => __( 'Parent Treatment:', 'nsc-treatments' ),
                    'not_found'          => __( 'No treatment found.', 'nsc-treatments' ),
                    'not_found_in_trash' => __( 'No treatment found in Trash.', 'nsc-treatments' ),
                ),

                // Frontend
                'has_archive'        => 'cosmetics/treatments',
                'public'             => true,
                'publicly_queryable' => true,
                'rewrite' => array('slug' => '%type%', 'with_front' => false),

                // Admin
                'capability_type' => 'post',
                'menu_icon'     => 'dashicons-screenoptions',
                'menu_position' => 20,
                'query_var'     => true,
                'show_in_menu'  => true,
                'show_ui'       => true,
                'supports'      => array(
                    'title',
                    'author',
                ),
            ) );
        }
    }

Answer 1

Your previous edit was a bit closer. Change the post type rewrite slug to:

cosmetics/treatments/%treatment-type%

Then change all instances of %type% to %treatment-type% in the treatment_permalink function.

Everything should then work correctly after you flush rewrites.

For future reference, the Monkeyman rewrite analyzer plugin is very helpful for debugging rewrite rules. As I mentioned, you can also dump the contents of $wp_query to see what WordPress is trying to query for in each request. You can put something like this directly in a 404 template for quick debugging of requests that you think should not be a 404:

<pre>
<?php print_r( $wp_query ); ?>
</pre>

You'll see a list of all query vars with their values and the resultant SQL query WordPress is sending to the database.