Yes, pinout here and connector type here:
https://docs.modalai.com/flight-core-datasheet-connectors/#j2---programming-and-debug-console
You need to make a little wiring harness to connect the JLink to J2
You don't need to the debug console (pins 2/3) for flashing, but if you are making a harness might as well and you can use it for debugging bootup if needed.
Download the bootloader here:
https://storage.googleapis.com/modalai_public/flight_core/bootloader/v5.0-167-g7bc2734/modalai_fc_v1_bl.bin
App here:
https://storage.googleapis.com/flight-core-firmware-1-10/latest/modalai_fc-v1.bin
You can download the JLink tools from the SEGGER website if needed.
You can use JFlash with a .jlink file with command like so:
erase loadbin foo/v5.0-167-g7bc2734.bin,0x08000000 loadbin foo/v1.10.0-15-g782a54bfd6.bin,0x08008000 r q x