We're at exactly the same stage you are at. We're migrating from a single virtual machine deployment and starting with SQL Server moving from the virtual machine to an existing enterprise grade SQL Server deployment.
My plan is to get a new database running and registered and test it for a few days until I am convinced it works, then lock the existing one and restore everything to the new one. After I am convinced the new one is functioning perfectly we shut take down the old one. It will probably sit around for a year before I finally delete it.
I've already confirmed with Esri that it's acceptable to do this both for licensing and technically.
After that I'm getting a 30 day temporary license so that the migration of Server and DataStore can go the same way, spin up the new components first and then after testing shut down the old ones.
10.9 has been sketchy for us, it's had some weird bugs bite us three times now. Our goal is to build a system divided into smaller pieces so it's easier to repair when it breaks again in the future. Right now it's all or nothing.