I installed CM 14.1 on a Nexus 6 and the first update booted into TWRP automatically to install but failed.
I manually installed the zip from the cmupdater folder and rebooted.
Now every time I try to reboot my phone or power it on from powered off it goes straight into TWRP.
Currently I have to boot into the bootloader and choose the Start option to get into my system.
Tried clearing dalvik/cache & internal storage in case something was cached somewhere. No dice.
Since you've already cleared your internal storage, I assume you backed up your important data already. In that case, flash a factory image and get a fresh start.
Just don't do CM updates via the built-in updater, it's designed to work well only with CM Recovery (which is pathetically weak).
EDIT: From your feedback it seems CM Recovery is what's required to finish the update (or at least get you out of the process). Just flash it and boot into it. Replace it with a recovery of choice later.
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