add_filter( 'term_link', array( $this, 'replace_term_link' ), 9000, 2);
function replace_term_link ( $termlink, $term ) {
    if( $term->taxonomy == 'product_cat' ) {
      $permalinks = (array)get_option( 'product_cat_custom_permalinks' );

      if( array_key_exists( (int)$term->term_id, $permalinks ) )
        $termlink = empty( $permalinks[$term->term_id] ) ? $termlink : $permalinks[$term->term_id];
    }

    return $termlink;
  }