Please don't give the usual response of 'try the troubleshooting guide' to flash the J-Link or Mbed firmware.
What I (and probably others) really need is the real initial bootloader firmware for the AT91SAM3U2 that shows up as the BOOTLOADER drive when the IF/BOOTRESET pin is pressed on power on. It seems that if the J-link operational firmware is corrupted, no amount of BOOTLOADER recovery seems to work to restore the J-Link. I'm able to restore the Mbed firmware but that just allows the device to show up as a USB drive to program the nRF52x code which is *not* what i need to do.
I've been unable to determine where the actual initial Mbed-enabled boot code is.
What i've done is cut SB31 and applied VDD to the ERASE pin of the interface MCU to get the SAM-BA bootloader interface connected. Then i've attempted to 'Enable Flash Access', 'Erase All Flash', 'Send File Name' with the .bin file for the J-Link firmware, and then finally 'Boot From Flash (GPNVM1)' before cycling power to the DK board. There's no detection of the USB link after that. I've obviously erased the initial Mbed bootloader because it doesn't appear anymore when IF/BOOTRESET is pressed during power on.
It seems to me there's the initial Mbed-enabled bootloader for the interface MCU which will boot into either the J-Link firmware or the Mbed firmware if they exist, but the J-Link and secondary Mbed firmware don't include the initial boot capability. I'd rather not have to get the Mbed development software and build my own since Nordic has already done it.