I would recommend a slightly different approach. It sounds like you want to upgrade from 4.0.3 to 4.1.6 and THEN move everybody to a new BES running 4.1.6.
The database schema between 4.0.3 and 4.1.6 is quite different. To preserve your data on BESMGMT, you need to upgrade the BES version first and then perform a Knife-Edge Cutover.
l0ki is right though.
KB05217 - Checklist for upgrading BlackBerry Enterprise Server software version 4.0 to 4.1
KB04261 - Perform a cutover to another BlackBerry Enterprise Server instance in an IBM Lotus Domino environment
When performing the actual cut over, DO NOT have oldBES running at the same time you bring up newBES. It's like crossing the streams. Egon says that's bad.