Edit the VM xml and change:
<clock offset='variable' adjustment='123456' basis='utc'>
The adjustment attribute takes any arbitrary value of seconds. Pick a random number of seconds from 0 to 900 (15 minute range). Let's see if also negative values are possible. I.e. a random number between + and - 900.
preventing Clock Correlation Attacks
make sure Qubes-Whonix has no access to clocksource=xen (T389)
Related Qubes upstream bug:
libvirt domain validation error; virsh edit issue