Teensy 3.2 bootloader connections

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What are the 2 additional connections to the bootloader on the 3.2 used for (compared to the Teensy LC)? One is also attached to pin 4 on the micro USB but I'm using a Type B connector and I'm having issues getting the board to be detected.
 
The sense pin shouldn't be doing anything, though best practice has it pulled low I believe. Have you been through the common issues with crystal wiring and Vbat here?

https://www.pjrc.com/store/ic_mkl02.html

And dumb questions, but these are bootloader chips from PJRC, not blanks? and you have pressed program after connecting to USB to get a first load of USB into the main chip?
 
Those 2 signals currently aren't used for anything at all.

Future bootloader versions might make use of them, though the one connected to pin 4 on the USB is very unlikely to ever be supported. Six years ago USB OTG seemed far more important than it does today.
 
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