From this article published in Motherboard, it really drives home the levels of paranoid secrecy Apple will go to:
If you take a phone with a cracked screen to the Apple Store, the Geniuses there don’t have to swap the button from your old screen to the new one. According to one current and two former Apple Store employees, there is a “Calibration Machine” in the back room of every Apple store that is able to reset the pairing between Touch ID buttons and the Secure Enclave. So when Apple replaces your screen, it simply recalibrates the new button to work with your existing phone.
“The calibration machine was a rather big device (imagine something roughly the size of a fairly large microwave) that phones had to be inserted into after replacing the display,” one former employee told me in an email. “It took about ten minutes per phone to calibrate them, and the device would run a battery of pressure-sensitive tests in addition to registering the display with the secure enclave. An iPhone had to be secured in the device, naturally, and a mechanical arm would perform the necessary functions.”
That’s mental. We can only imagine what really goes on inside that magic box since it’s evidently completely secured whilst it does its thing.
Maybe there’s a gang of iKittens going to work and controlling the mechanical arm… mechanical paw?
Anyway, go and read the full article, it makes for a fascinating read.
Update (14th March 2017): Mystery solved! Kind of.