Due to DataDomain architectural limitation you cannot enable DD Boost on existing storage unit that's why you need to create a new storage unit. There is no instruments to migrate files from one storage units to another.
Keep in mind that Veeam will initiate active full however all data will be deduplicated by DD Boost on the proxy and you won't notice high network saturation between Veeam backup proxy and DataDomain server.
Also you need to remove old backup chain manually once you decide you no longer need it. In order to remove it go to backups and find your backup chain on the CIFS/NFS repository, right click on it and select "Remove from backups"