BES 4.0 with Exchange 2003 SP1. Installed SP3 & HF2 last night. No problems. We run BES on a DL 360 with mirrored volume. I just removed one of the mirrored hard drives and put that away as a backup for recovery if necessary, performed the updates, checked & tested, then inserted another blank disk in place of the one I removed. Updates were successful and BES services and the Server itself are running within optimal parameters. I still have the backup drive just in case.
James