Anil Eklavya:
To my knowledge, Qubes Backup backs up root and private volumes of
selected VMs, their definitions from qubes.xml, their templates, and
dom0 ~/*. If I suspected compromise though (are you sure the screw
wasn't just stripped and fell out somewhere?), I wouldn't trust backups
made from it either. Restoring AppVMs to a new machine from backups made
prior to compromise would be safest if you know exactly when it
happened, and that the backup media hasn't been tampered with. You could
maybe use rsync to copy the potentially infected files out, but make
sure it's by itself on a dedicated network behind a firewall that only
permits rsync connections to the rsync server. Other option would be to
pull the hard drive, attach it to a USB-SATA converter, and very
carefully mount it on a known good machine in a disposable VM without a
network connection to extract the (possibly bad) data. Then, securely
dispose of the laptop and hard drive. Make sure to use new passphrases
on the new hardware in case a keylogger was installed on the old.