You are not supposed to copy the .pacnew over the existing configuration file, but to merge the new file in, i.e. to wisely adapt your existing file with the changes proposed in the .pacnew.
In the case of encryption, you need to include the sd-encrypt hook. Also, the keymap and consolefont hooks are no longer needed when sd-vconsole is used.
See… 
Your new /etc/mkinitcpio.conf should look as follows…
FILES=(/crypto_keyfile.bin)
HOOKS=(base systemd keyboard autodetect microcode kms modconf block sd-vconsole plymouth sd-encrypt filesystems)