Most updates do not change the database and also do not change the config file format. In those cases, you could back-up the content of db subfolder and of config.xml, then do the update. Then stop the server (it ill start indexing but it is safe to stop it), then restore the old config.xml and db folder and then start it again.
Please note that we advertise support for up to 100,000 items, and while we fully expect 1,000,000 to work we do not test such library sizes on regular basis. I am curious if your huge library even works with other servers.. can you share your experience?