I hope I'm not too late to contribute.
Before an upgrade to BlackBerry Enterprise Server software version 2.2 to 4.0 or later, you need to perform these steps so as to allow synchronization capabilities to be added to the state database, and also allow the wireless service books to be sent to the BlackBerry device:-
1. Upgrade BlackBerry Device Software to version 4.0 or later.
2. Connect the BlackBerry device to a computer running BlackBerry Desktop Manager version 3.6.3 or later (it is recommended to upgrade to version 4.0 or later).
The BlackBerry Enterprise Server for IBM Lotus Domino Version 4.1.2 Upgrade Guide states that BlackBerry devices with BlackBerry Device Software version 4.0 or later must be connected to BlackBerry Desktop Manager Version 3.6.3 or later before upgrading the BlackBerry Enterprise Server.
Otherwise you will some problems to tackle. See KB12982 - Prepare BlackBerry devices before upgrading to BlackBerry Enterprise Server software version 4.0
for more information.