Since you'll be migrating to a new VC, you will need to discover the new VC, re-import the clients under the new VC and re-register/redeploy the avamar proxies as they will now be tied to the new VC. We have done this in the lab and it's pretty straight forward.  The Avamar Administrator Guide will guide you thru modifying the mcserver.xml to allow multiple VC's so you can leave your current guest backups alone until they age out of the system. One other note, because of the migration to a new VC, Avamar may look at these as "new" hosts and need a full scan upon initial backup on the first backups thru the new VC.  Are you using converter to batch migrate or some other methodology ?
Lookig for sugestions on best method to upgrade a vSphere 4 enviornment to vSphere 5 and its impact on Avamar. Specifically what has to be done to the Avamar enviornment to support this. Specifically looking to build new vCenter, migrate ESX hosts into it then upgrade the esx host. What impact will this have on a pre-exisiting avamar enviornment?
Upgrading vSphere 4 to 5 and Avamar