debian updates with "sudo apt-get update && sudo apt-get dist-upgrade"
Whonix should be the same, ("apt-get" or "yum"), but Im not entirely sure.
Keep an eye on your logs (journalctl) and your RPC Policy.
Your RPC Policy suggests that Whonix will update through Tor,
$tag:whonix-updatevm $default allow,target=sys-whonix
so make sure sys-whonix is running.
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