How to set order for a custom post type

As @Pat said, pre_get_posts is action hook, it wont work that way. But you don’t need to use pre_get_posts hook in functions.php.
Remove this functions and filter from functions file and use these arguments in you WP_Query. orderby instead of ID, use menu_order.

$args = array(
    'post_type' => 'bxslider',
    'orderby' => 'menu_order',
    'order' => 'ASC',
    'posts_per_page' => -1,
    'ignore_sticky_posts' => 1,
);