If you do a new install with a new VC database, then you will lose things like user permissions, HA/DRS setup, resources pool setup, etc when you move the hosts to a VirtualCenter server. You would also have to put ESX hosts that are part of a cluster in maintenance mode to move them.
You might instead want to consider just swaping out the current VC server with the new one. This will be fairly easy if the database for VC is on a another server already. If that's the case the you would need to shutdown the current host, install on the new with the same IP / hostname as the old one. When you come to the db setup portion of VC, you would use the existing database being careful not to overwrite the contents of the existing db. Once the server install would be done, you would reboot and it would function is place of the old server.
