We've never used the JTAG pins on the Duet, so when we needed to revise the layout of that area to reduce EMI, we were happy to remove the connector. If we wanted to do hardware debugging now, we would use Serial Wire Debug instead of JTAG, as we do on Duet 3. For Duet 2 we'd need to build a firmware variant that doesn't reprogram the bus matrix to use the SWD pins as GPIO pins.