How to cleanly reboot core OS when "Failed to talk to init daemon" is seen?

kill -15 1

That should wake up the init daemon and then you should be able to reboot as normal. (i.e. sudo kill -15 1; sudo reboot)

If possible, this is a better solution than reboot -f as you will be able to perform a clean reboot.

sudo reboot -f

-f, --force Force immediate halt, power-off, reboot. Do not contact the init system.