You've done all the software things you can do to make sure macOS is up to date and running, but the Touch ID runs on a separate computer and not the main system. This part is the T2 chip and your fingerprint gets registered in to the Secure Enclave - not on the main OS or storage. The T2 also controls the Touch Bar - so this procedure works to remedy issues there once you've verified it's not SMC or macOS causing the glitch.
I would make sure you have a good backup since one of these steps will guarantee everything is erased on the drive if you follow all the steps below. Nothing will be recoverable, not from vendors or undelete software - the data will be cryptographically erased / sanitized / destroyed.
The above guide will walk you through the steps once you attempt to revive (or erase/restore) the Apple T2 Security Chip firmware. Revive just reloads the T2 and restarts it. Restore erases everything - all data keys, all fingerprints, everything - complete factory reset of your Mac. The first link us unlikely to change - search for the Apple Configurator user guide if these links change as the document gets updated (or you prefer a different localization / language than English).
If you are not comfortable loading your backup and reinstalling the Mac operating system, you might want to have a trained tech do the work in Apple Configurator and the person restoring / reviving needs a second Mac to connect and update your Mac firmware.
For your MacBook Pro - the steps to prepare it for the revive (which is less invasive - I would try that first) is as follows:
Prepare the Apple portable computer to revive the firmware
- Press the wake/sleep button for about 5 seconds to shut down the Apple portable computer.
- Plug the cable into the right Thunderbolt port on the left side of the Apple portable computer.
- While holding down the power button, at the same time press all three of the following keys for about 3 seconds: Right Shift key +
Left Option key + Left Control key
Note: You won’t see any screen activity from the Apple portable computer.
Also, be sure you have the time to do this - I would set aside 35 minutes to get ready and then print out your steps, take a break and then allow an hour to try this the first time. When the instructions say 5 seconds - I would have a clock and be like someone defusing a bomb - precise, exact. If it says right key - the left one will not do, etc...
Once you've got Apple Configurator - all the exact cables, this can be done in 15 minutes for the first Mac and then 5 to 8 minutes for each Mac of the same type you need to work on, but give yourself time the first pass and be sure your backup drive is ready and tested. If you choose the wrong "r" command - you will not get a chance to stop the erase - it happens in an instant.
