so, IIUC, SME is a VB host and you'd like to backup its virtual guests using affa, am I right?
as long as you suspend the VMs with a pre backup script (and restart them with a post backup one), I can't see any issue..
be aware that virtual disks are likely not copied, because, from an external point of view, they don't change.. this is false only if you're using dynamic disks and they grow..
before starting, I suggest you to search for "rsync and virtual disk" with google