Yes, I see, cloning VDR with it's destination disks attached will also clone the backup stores.
I'm just use to looking at it another way. Rather than seeing VDR and the backup stores as a VM with big drives, I see a self contained applicance that is easy to restore from CD and potentially many backup stores on shares or virtual disks. So I clone just the backup stores when I want to be safe. If your backup store's catalog goes bad, you go to the backup store copy (if repair efforts fail). If your VDR goes bad (but not necessarily your backup stores), then you reinstall VDR.
So my problem becomes how to duplicated virtual disks and network shares from my backup device onto something that can be archived like a USB hard drive. That depends on where you can attach your USB drive. I can hook it directly to my backup device which is a NAS. If the VDR backup store is a CIFS share, I can run a backup job (not VDR) on my NAS that copies the backup store directly to the USB drive. If the backup store is a virtual disk, that should work too but I use thin provisioned disks since all my datastores are NFS accessed. I found that some of these backup programs will expand it to a fully provisioned disk so the copy is very slow. You can also use the vCenter Datastore browser to copy vmdk files. I have found however to preserve thin provisioning you have to copy just the vmdk file and not the containing folder which is odd.
What I really want to be able to do is daily backups with VDR to my NAS and a weekly backup to an external hard drive that I can put away somewhere safe. So rather than copy the backup store, I want to create it on the external hard drive by using a VDR backup. Well, I've tried to hook an external drive to Iomega (using USB), ReadyNAS (using USB), and QNAP (using eSATA) and it mostly succeeds. But there is something quirky about NFS sharing an external hard drive on these NAS units and I get frequent -2246 errors in VDR when mounting them. Sometimes they mount properly, sometimes not.
So this time I'm trying a new idea. I finally figured out how to use USB device passthrough from ESXi 4.1 to VDR. I've got a backup job running to the USB drive now and I'll record the performance. I'll also be looking out for quirky mounting problems. If reliable, this would also be a good way to copy backup stores. Just mount your backup store disk, then mount your USB disk to VDR using the ESXi passthrough, make sure VDR hasn't spawned an Integrity check, and do a "cp - Rv $src_mount/VMwareDataRecovery $dest_mount/".
Sorry I'm so verbose. I'm trying to figure out the best way too.