When updating package linux / linux-lts or kernel modules needed at boot time, like ZFS, the mkinitcpio is only generated before dkms rebuilds the modules for the new kernel / the new modules, so when rebooting, boot will fail because of missing kernel modules for access to the root filesystem. So after an update to one of the mentioned packages, you need to manually run mkinitcpio -p linux to get a bootable system.

The problem is already reported as bug in the Arch Linux pacman bug tracker: https://bugs.archlinux.org/task/49052.