DELETE
FROM yourDatabaseName.menu_links
WHERE menu_name LIKE 'main-menu'
AND depth > 2
AND plid != 597

/**
 * Hide old menu item.
 */
function module_name_update_7000() {
  db_update('menu_links')
    ->fields(array('hidden' => '1'))
    ->condition('menu_name', 'main-menu', '=')
    ->condition('p1', '5947', '=')
    ->execute();

  drupal_flush_all_caches();
}