Was reading the BES install guide and saw this sentence. Just incase it helps you:
"If any instances of the Blackberry Enterprise Server version 3.63 or later exist that have never been added to the Blackberry Manaer, you must add them or remove them before starting the upgrade procedure. If servers exist that have not been added to the Blackberry manager, the database update cannot be completed and the upgrade process fails."
History: PB32, 9800, 9700, 8310, 8700, 7100r, 7780, 7280, 6710, 957, 950