May only be Qubes 3.1. May only be Whonix and not all Debian templates.
Be ready with
qvm-revert-template-changes. It can be used after reboot as long as the templateVM has not been started again.
My default NetVM is sys-whonix. On boot, sys-net hangs in yellow state, sys-whonix goes to green but is unable to run any processes. (Irrelevant) Checking kern.log via xl console, shows that mounting-dirs service is unable to start, resulting in no mounting of /home/user/ and a broken KDE.