I’ve had a quick Google and the standard answer seem to be to adjust the Global Settings, but that isn’t working.
When I run an update, the updates seem to be triggering Whonix to start and running that VM.
I have installed a VPN proxy VM, and would prefer that traffic went through that as it saves on having to run another VM. However I can’t find any setting or control to do this. I’ve made the adjustment in the Qubes Manager but it still seems to be going through Whonix.
The answer to this depends on how you are using your VPN, and where it
is positioned in the network order.
The proxy to use is configured in /etc/qubes-rpc/policy/qubes.UpdatesProxy - my guess is that you have
this configured to use sys-whonix. Just change that to use the proxy you
want.