Anil Eklavya:
Can someone clarify exactly what all does Qubes Backup save and restore? To
me this is important because I am fairly sure my Qubes installation has
been compromised, if not at dom0, then certainly for some VMs, including
sys-net (which includes sys-usb). Most probable reason is Evil Maid Attack
as I found one screw on my laptop missing, which was earlier there. I know
this attack could be accomplished even without opening the laptop up, but
someone might have tampered with the laptop and may also have used the USB.

In such a case, if I backup and restore to a new installation, will the VMs
still be compromised because they will be restored completely, or will they
be fresh in the sense that only my data will be restored, along with a few
basics like the specification of VM?

Will it be preferable to use something like rsync for taking separate
backups of the data on VMs?

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.

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