To purge remaining caches after user traffic cutover to new code:

  php admin/cli/purge_caches.php --muc
  php admin/cli/purge_caches.php --js
  php admin/cli/purge_caches.php --filter
  php admin/cli/purge_caches.php --other

You should perform these purges in isolation, with a gap between commands, to reduce load spikes on the web server.