I would recommend you make sure you have Desktop Manager verison 4.2, Service Pack 2, loaded to your PC. What PC OS are you running?
The reload of the user data to the BB can take a while, according to size of the messaage database and the call log database, especially. Before upgrading the OS, I would recommend at least minimizing the call log database by deleted most of your call logs, as welll as many messages as you can. A reload should take 20-30 minutes, and I have seen some with large message and call log data take over an hour.