Just did the upgrade both Windows server 2003 32-bit and domino 8.5.2 32-bit to 64-bit version.
After all it run well, then I found this technote.
Duh, I hope I found that technote much more earlier, before I upgrade my windows and domino into 64-bit version, that will make it a lot easier.
Please take a special attention on point seven (or six), “7. Before restarting the Domino server, run the offline maintenance on the following system databases from command prompt.”
If you have a large domino databases, and you have only limited down time, than copy entire domino data directory may be is not an option. In my experience, copy 1,2 TB of domino data will take more than a day. And after we start the new server, it give a lot of error messages and the fixup process run almost on all databases.
So we did it with another way, we create a additional server, create replica of all databases to the new server, and after that we only need to switch server id. It take a longer time to replicate (almost a week), but the down time is minimum, less than a hour.
So, which way is your choice, either copy the data all create replicas.