I rarely ever have problems with Arch Linux updates, but the other day, KDE crashed while pacman was running and the system would not boot after that, even though I restarted pacman to finish the upgrade. The fact that KDE does not crash more often during upgrades is amazing as you are replacing a bunch of stuff that is currently being used in a running system. After booting from an install disk, it appeared entries from the /boot directory were missing. I re-ran the linux package install, and that seemed to fix things up.
I think in the future, I’ll run pacman inside of tmux – that way if the GUI crashes, pacman will keep running and have a better chance at finishing.