After the upgrade my system would not boot. I got a message: "loading initial ramdisk" and it was just stuck there.
This turned out to be because I'm running and encrypted system (with lvm) and the boot process wasn't expecting an encrypted system.
I was able to boot into my system by editing the Grub 2 boot menu entries and added the special Grub commands for booting an encrypted system. https://wiki.archlinux.org/index.php/GRUB#Encrypted_GNU.2FLinux_menuentry (It seems there are at least three ways to configure an encrypted system to boot: the regular method with the encrypt hook in mkinitcpio, the systemd method, and the Grub 2 method--I have no idea if one is better than the other).
After I got into my system, I ran mkinitcpio and this configured a proper initramfs.
My question is, why did this get messed up in the update process? Shouldn't have the updates to the kernels (I have 4.9 and 4.11 installed) run mkinitcpio and generated a proper initramfs? Neither kernel would boot after the update.
One other factor: I saw there was the new 4.12 kernel and after I ran the update I installed that kernel using the Manjaro Settings Manager. After that I rebooted and 4.12, 4.11, and 4.9 all got stuck at "loading initial ramdisk."
I vaguely recall that I may have had this problem once before. That if after an update I rebooted my system first and then installed a new kernel with Manjaro Settings Manager, it was fine. But If I installed the new kernel before I rebooted my system I got this problem. (I'm not 100% sure of this recollection.)
Anyway, why should it matter when I install the new kernel after an update and if that's not the issue, why would mkinitcpio not run properly during an update?