You could just upgrade the 3.6 installation to 4.1 and then install the other 4.1 BES servers to point to that same database and move users between the servers at will with no user interaction and very little disruption (no handheld wipes, no reactivations initiated by the users - there is a short enterprise activation that happens automatically on the device).
Just a suggestion - might make life a bit easier (or it could have a botched upgrade and you'd be in a bad place, but...).