Hello and welcome to the Forums!
When you build out your new vCenter Instance are you using a new hostname and ip address? If so, from your old vCenter Instance you can right click on the hosts and disconnect. Once they are disconnected you can then remove them and their guests. From there go to your new vCenter instance and add host. During the move, not guests will be impacted.
If your licensing server for your VI3 Hosts is on the old instance, you can leave the license server running and just shutdown the vCenter Server Service. Otherwise you can build a standalone license server on your new host.
This is a very high level. Let us know if you need more information.