ちなみに「pacman -Syu」でのアップデートですよね？mkinitcpioが失敗したということですかな。/var/log/pacman.logに以下のような記述はありますか。最新のビルドの出力とその前のビルドの出力を比較すると何か分かるかもしれません。
[2017-02-25 01:38] [ALPM] running '99-linux.hook'...
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Starting build: 4.9.11-1-ARCH
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [base]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [udev]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [autodetect]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [modconf]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [block]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [encrypt]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [filesystems]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [keyboard]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [fsck]
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Creating gzip-compressed initcpio image: /boot/initramfs-linux.img
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Image generation successful
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux-fallback.img -S autodetect
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Starting build: 4.9.11-1-ARCH
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [base]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [udev]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [modconf]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [block]
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: aic94xx
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: wd719x
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [encrypt]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [filesystems]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [keyboard]
[2017-02-25 01:38] [ALPM-SCRIPTLET] -> Running build hook: [fsck]
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Creating gzip-compressed initcpio image: /boot/initramfs-linux-fallback.img
[2017-02-25 01:38] [ALPM-SCRIPTLET] ==> Image generation successful「ERROR: module not found」とかが混ざっていませんか。それと手動で「sudo mkinitcpio -p linux」を実行してどんなエラーが出るか見てみたいです。