Export your 3.6 server from 3.6 the manager.
Import 3.6 server to the 4.0 manager
When you import the server, all users should show up.
Change the database settings in the properties of BlackBerry Server Management to point to the 4.0 database.
Change the ODBC BESMgmt connection to point to the 4.0 database.
*You may now only manage the 3.6 server from the 4.0 database.
If you have IT Polcies you may have to re-create (if they dont already exist) or re-assign them.
You may then upgrade to 4.1.
It is also required that both servers be offline for the initial upgrade to 4.1 as the database schema is modified.
Also note that the user limit for an MSDE database is 500 (total), you will also have to move to SQL. How To - Move the BlackBerry Configuration Database from one server to another