OK, you can't point a 4.1 BES at a 3.6 database, the tables are different and it simply won't work.
Are you going to run the new instance of BES on the same machine? If so then just upgrade if you want. If not then export the user list from the 3.6 BES, install the new 4.1 instance on the new BES (shut the old one down first), then import the user base list in to the new instance. If the devices are all 4.0 or above they will reactivate themselves.
If it were me and if I was keeping it on the same box I'd go for a fresh install to be honest. Again, export the user list, uninstall the 3.6 instance, install the new 4.1 instance and then import the user list.