Thanks for your advice, some good pointers there and it's helped me get the best course of action clear in my head. I've not migrated a BES to a new server before and while Blackberry's docs are good on technical detail I don't find them particularly helpful in giving an overview of what to do!
With your help I've found some detailed info on how to backup the MSDE database with OSQL at BlackBerry Search Results
so I'll give that a try.
One thing I'm still not clear on is if I export the MSDE 7 database on the BES 3.6 server and then import it to MSDE 2000A on the BES 4.0 server, will it work, or does the BES 3.6 server need to be upgraded to MSDE 2000A first? And, if I have to upgrade it to MSDE 2000A, will just installing it from the package retain and automatically upgrade my database?