Consider using borgbackup.

Borgbackup is bandwidth-efficient (only sends deltas), versioned (later backups 
don't overwrite earlier ones), compressed, deduplicated, and encrypted.

Here is an outline of a Qubes 4.0 setup:

BACKUP:
In dom0, borg reads the source VM's private block device and computes the delta 
(of the raw data) against all previous backups. The delta is then compressed, 
encrypted, and then streamed to a net-connected VM, which in turn ssh's the 
data to your backup server.

RESTORE:
In dom0, borg again uses the net-connected VM to mount a FUSE fs (in dom0) 
containing the block device you backed up. You then pass that block device to 
the source (or other) VM (via loop mount + qvm-block). Inside the VM, you mount 
the device read-only, and can now restore single files or rsync all files 
(restores differences!).

For example, a 20GB backup may result in a 200MB daily delta that takes 5 
minutes to backup remotly.

SECURITY:
* At no point does decrypted data leave dom0. The encryption key stays in dom0. 
Neither the remote server, nor the net-connected proxying VM, are trusted.
* You never mount the backup in dom0, only in the source or other VM
* Since the backup is orchestrated by dom0, the source VM cannot delete its own 
backups.

IMPLEMENTATION NOTE:
The key to using borg from dom0 is to use BORG_RSH= to tunnel out, something 
like
  BORG_RSH='qvm-run -p <borg_proxy_vm> ssh'
(This doesn't quite work since dom0's qvm-run doesn't pass extra args to the 
command it runs, but you can workaround it using a script).

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