function prefix_reset_metabox_positions(){
  delete_user_meta( wp_get_current_user()->ID, 'meta-box-order_post' );
  delete_user_meta( wp_get_current_user()->ID, 'meta-box-order_page' );
  delete_user_meta( wp_get_current_user()->ID, 'meta-box-order_YOUR_CPT_SLUG' );
}
add_action( 'admin_init', 'prefix_reset_metabox_positions' );