I don't know the specifics, but when you -Syu and there's a kernel update, at the end of the update it will run some additional commands. I'm pretty sure that's normal pacman behaviour, but I haven't used vanilla Arch in a while. At that point mkinitcpio would fail silently, I couldn't boot afterwards, and there were no warnings about it. Running the command manually would work without an issue and allow me to boot again.