we've had a few planned powerdowns for our systems, once for moving server rooms, another to clean the room out from dust/crap from a construction project. Just make sure you shut down the BES first, then mail server, then domain controller(s). Then reverse that order when powering up. Power up domain controller(s), let them fully power up and all services start, then power up mail server, make sure the mail server is functioning properly, then power up the BES.
If you do it something like that you generally shoudln't have a problem.
BES 5.0.2 MR4
Exchange 2010 SP1 RU2
WES 2008 Alumni