404 when remove Slug base custom taxonomy and custom post type

I have a custom taxonomy (cities) and a custom post type (spots). I have removed the custom taxonomy base slug and the custom post type base slug to have this :

• 
  

  mysite.com/amsterdam (all spots in amsterdam)

  
  


• 
  

  http://ift.tt/1zuX53M (a spot in amsterdam)

  
  

I have also do a custom permalink for all posts to have a blog (in option permalinks) : http://ift.tt/1Ajri8N

Today, custom taxonomy and custom posts urls works but i have 404 errors for all my blog posts and pages.

Here is my custom function.php:

/**
* Register a custom post type SPOTS
*/
function custom_post_type_spots() {

$labels = array(
    'name'                => _x( 'Spots', 'Post Type General Name', 'text_domain' ),
    'singular_name'       => _x( 'Spot', 'Post Type Singular Name', 'text_domain' ),
    'menu_name'           => __( 'Spots', 'text_domain' ),
    'parent_item_colon'   => __( 'Parent Item:', 'text_domain' ),
    'all_items'           => __( 'All Items', 'text_domain' ),
    'view_item'           => __( 'View Item', 'text_domain' ),
    'add_new_item'        => __( 'Add New Item', 'text_domain' ),
    'add_new'             => __( 'Add New', 'text_domain' ),
    'edit_item'           => __( 'Edit Item', 'text_domain' ),
    'update_item'         => __( 'Update Item', 'text_domain' ),
    'search_items'        => __( 'Search Item', 'text_domain' ),
    'not_found'           => __( 'Not found', 'text_domain' ),
    'not_found_in_trash'  => __( 'Not found in Trash', 'text_domain' ),
);
$rewrite = array(
    'slug'                => '%cities%',
    'with_front'          => false,
    'pages'               => false,
    'feeds'               => false,
);
$args = array(
    'label'               => __( 'spots', 'text_domain' ),
    'description'         => __( 'All Spots', 'text_domain' ),
    'labels'              => $labels,
    'supports'            => array( 'title', 'editor', 'excerpt', 'thumbnail', 'trackbacks', 'revisions', 'custom-fields', ),
    'taxonomies'          => array( 'cities' ),
    'hierarchical'        => true,
    'public'              => true,
    'show_ui'             => true,
    'show_in_menu'        => true,
    'show_in_nav_menus'   => true,
    'show_in_admin_bar'   => true,
    'menu_position'       => 5,
    'menu_icon'           => '',
    'can_export'          => true,
    'has_archive'         => false,
    'exclude_from_search' => false,
    'publicly_queryable'  => true,
    'rewrite'             => $rewrite,
    'capability_type'     => 'post',
);
register_post_type( 'spots', $args );
}
add_action( 'init', 'custom_post_type_spots', 0 );


/**
 * Register Custom Taxonomy CITIES
 */
function custom_taxonomy_cities()  {
$labels = array(
    'name'                       => _x( 'Cities', 'Taxonomy General Name', 'text_domain' ),
    'singular_name'              => _x( 'City', 'Taxonomy Singular Name', 'text_domain' ),
    'menu_name'                  => __( 'Cities', 'text_domain' ),
    'all_items'                  => __( 'All Cities', 'text_domain' ),
    'parent_item'                => __( 'Parent City', 'text_domain' ),
    'parent_item_colon'          => __( 'Parent City:', 'text_domain' ),
    'new_item_name'              => __( 'New City Name', 'text_domain' ),
    'add_new_item'               => __( 'Add New City', 'text_domain' ),
    'edit_item'                  => __( 'Edit City', 'text_domain' ),
    'update_item'                => __( 'Update City', 'text_domain' ),
    'separate_items_with_commas' => __( 'Separate Cities with commas', 'text_domain' ),
    'search_items'               => __( 'Search Cities', 'text_domain' ),
    'add_or_remove_items'        => __( 'Add or Remove Cities', 'text_domain' ),
    'choose_from_most_used'      => __( 'Choose from Most Used Cities', 'text_domain' ),
);

$args = array(
    'labels'                     => $labels,
    'hierarchical'               => true,
    'public'                     => true,
    'show_ui'                    => true,
    'show_admin_column'          => true,
    'show_in_nav_menus'          => true,
    'show_tagcloud'              => false,
    'rewrite'                    => array('slug' => 'cities'),
);

register_taxonomy( 'cities', 'spots', $args );
}
add_action( 'init', 'custom_taxonomy_cities', 0 );

/**
 * Remove the slug from published post permalinks.
 */
function spots_remove_cpt_slug( $post_link, $post, $leavename ) {
    if ( 'spots' != $post->post_type || 'publish' != $post->post_status ) {
        return $post_link;
    }
    $post_link = str_replace( '/' . $post->post_type . '/', '/', $post_link );
    return $post_link;
}
add_filter( 'post_type_link', 'spots_remove_cpt_slug', 10, 3 );


function custom_parse_request_tricksy( $query ) {
    // Only noop the main query
    if ( ! $query->is_main_query() )
        return;

    // Only noop our very specific rewrite rule match
    if ( 2 != count( $query->query ) || ! isset( $query->query['page'] ) ) {
        return;
    }

    // 'name' will be set if post permalinks are just post_name, otherwise the page rule will match
    if ( ! empty( $query->query['name'] ) ) {
        $query->set( 'post_type', array( 'post', 'spots', 'page' ) );
    }
}
add_action( 'pre_get_posts', 'custom_parse_request_tricksy' );

function wpa_spots_post_link( $post_link, $id = 0 ){
$post = get_post($id);  
 if ($post->post_type != 'spots')
    return $post_link;

if ( is_object( $post ) ){
    $terms = wp_get_object_terms( $post->ID, 'cities' );
    if( $terms ){
        return str_replace( '%cities%' , $terms[0]->slug , $post_link );
    }
}
return $post_link;  
}
add_filter( 'post_type_link', 'wpa_spots_post_link', 1, 3 );