I have a custom post type called "nutrix-recipe".

It has a lot of taxonomies, for example "nutrix-category" or "nutrix-tag".

In post_edit.php, I removed all taxonomy meta boxes and added select2 fields to allow selection of terms. This works so far. The meta is saved.

This is, for example, how nurix-category is displayed inside the display_metbox function:

// CATEGORIES FIELD
    $html = '';  
    $label = __( 'Category: ', 'nutrix' );
    $current_tags = get_post_meta( $post_object->ID, 'nutrix_select2_categories',true );

    if( $categories = get_terms( 'nutrix-category', 'hide_empty=0' ) ) {
        $html .= '<div class="nutrix-div-20"><p><label for="nutrix_select2_categories">' . $label . '</label><br /><select id="nutrix_select2_categories" name="nutrix_select2_categories[]" >';
        foreach( $categories as $category ) {
            $selected = ( is_array( $current_tags ) && in_array( $category->term_id, $current_tags ) ) ? ' selected="selected"' : '';
            $html .= '<option value="' . $category->term_id . '"' . $selected . '>' . $category->name . '</option>';
        }
        $html .= '</select></p></div>';

        echo $html;
    }

This is the nutrix-tag display:

// TAGS FIELD
     $html = '';  
     $label = __( 'Tags: ', 'nutrix' );    
     $current_tags = get_post_meta( $post_object->ID, 'nutrix_select2_tags',true );
    if( $tags = get_terms( 'nutrix-tag', 'hide_empty=0' ) ) {
        $html .= '<div class="nutrix-div-40"><p><label for="nutrix_select2_tags">' . $label . '</label><br /><select id="nutrix_select2_tags" name="nutrix_select2_tags[]" multiple="multiple" >';
        foreach( $tags as $tag ) {
            $selected = ( is_array( $current_tags ) && in_array( $tag->term_id, $current_tags ) ) ? ' selected="selected"' : '';
            $html .= '<option value="' . $tag->term_id . '"' . $selected . '>' . $tag->name . '</option>';
        }
        $html .= '</select></p></div>';

        echo $html;
    }

I save them this way (nonce is missing atm):

function nutrix_save_recipe_mb( $post_id, $post ) {

    if ( defined('DOING_AUTOSAVE') && DOING_AUTOSAVE ) return $post_id;

    // if post type is different from our selected one, do nothing
    if ( $post->post_type == 'nutrix-recipe' ) {
        if( isset( $_POST['nutrix_select2_categories'] ) )
            update_post_meta( $post_id, 'nutrix_select2_categories', $_POST['nutrix_select2_categories'] );
        else
            delete_post_meta( $post_id, 'nutrix_select2_categories' );

        if( isset( $_POST['nutrix_select2_tags'] ) )
            update_post_meta( $post_id, 'nutrix_select2_tags', $_POST['nutrix_select2_tags'] );
        else
            delete_post_meta( $post_id, 'nutrix_select2_tags' );
}
}

All these work. But my problem is, that the taxonomy terms are not assigned to the post. Or from another view: If I visit the edit tags page, the category count remains zero.

Is it possible to not only save the meta, but also set the taxonomies ?

Thank you :)