Which version of Whonix?
It sounds like a similar issue as described here Whonix VirtualBox 14.0.0.5.5 Testers Wanted! - #17
though not 100% the same. In my case the boot was just delayed and it didn’t drop to an initramfs shell.
You could try the following: On the gateway after the updates have been installed but before rebooting do:
echo "RESUME=none" > /etc/initramfs-tools/conf.d/resume
then do:
update-initramfs -u -k all
Reboot.
Also during the upgrade look for anything odd and/or initramfs related.
2 Likes