I’m interested in an authoritative response on this as well.
In my experience, when the BES server loses connection to the database, the Console is unusable, downloads may not process, and client reports are not imported. When the database comes back online, the root server reconnects after a minute or so and everything catches up.
If I had to venture a best practice guess, I’d patch the root server and database server on a separate schedule from your other systems; and try to precache as many of your downloads as possible so the database server doesn’t have to request more downloads while the BES server is offline or disconnected from DB. (Downloads will eventually process later if not precached, but might make your patch window larger).
Precaching is as simple as making sure your download cache client settings are large enough, and issueing your actions with a “start time” set in the future and “begin downloads before constraints are satisfied” checked on the Take Action dialog.