This is the repo which contains all the files that were used to flash the HHKB Pro Classic with QMK as well as some of the stuff used when creating the Yamamech HHKB userspace code.
In order to flash the board with this firmware using dapboot, the board needs to enter recovery mode, which can only be done by tearing the board down, removing the metal shield on the back of the controller board, and then bridging the right side of R6 and R85 while the board is being plugged in. The easiest way to do this is to use a jumper wire with the board unplugged, and then plug the board in while the wire is connected. If done correctly, the board's LED (which requires the controller to be connected to the other PCB) will glow orange. Then you can use DFU to flash the custom dapboot.bin, which can be found either at the original fork or in my HHKB resources repo. Once this has been flashed to the board you can enter the DFU mode without needing the jumper wire by using the shortcut LShift+RShift+Esc. Lastly, now you can flash the board as you normally would with QMK: qmk flash -kb hhkb/classic/dapboot -km yamamech. I've not been able to get the non-dapboot firmware to flash successfully, however if this does work for you then you can skip the flashing of dapboot, however you won't be able to reset the board to DFU mode without jumping the wires (or possibly adding a QK_BOOT bind, however as I can't get the board to work without dapboot I can't confirm if this will work or not)