Yubikey no longer works when logging in

Running OS 10.14 (Mojave) on my MacBook Pro 2017 with Touch Bar. I configured it to require Yubikey 4C when logging in or the screensaver was on the day after Mojave was released.

Today, I rebooted my Mac and I’m no longer able to login.

I use FileVault 2, so I’m prompted for my password twice. I enter it the first time (no Yubikey required) and it progress bar appears. Once it’s almost done, the screen flashes black, the Apple logo and progress bar appear, and then I’m at the login screen a second time. Here I plug my Yubikey into a USB C port. It briefly lights up, I enter my password, but I’m not allowed to proceed.

I the Yubikey has worked to login in the past and all four USB C ports on my MacBook Pro are working fine with other devices.

To fix this, so far I’ve

-tried both of my Yubikeys into all four USB ports, trying each side in both sides

-reset the SMC

-reset the PRAM

-booted up in recovery mode and ran Disk Utilities

-booted up in recovery mode and tried to uninstall Yubikey via Terminal

-tried to login in Safe Mode

-booted up in recovery mode and tried to create a new user account

Any suggestions before I restore from Time Machine? Thanks!