For VMs managed by vCloud Director, Veeam Backup & Replication offers a special type of the backup job — vCD backup job. vCD backup jobs have been specifically developed to process vCloud Director objects, ensure their proper restore and support of vCloud-specific features.
You should always use vCD backup jobs to back up VMs managed by vCloud Director. If you back up VMs managed by vCloud Director using a regular backup job, Veeam Backup & Replication will perform backup at the level of the underlying vCenter Server and will not capture vApp metadata. As a result, you will not be able to restore a fully-functioning VM to vCloud Director.