Ok so looking at the tiny text on the controller, the mcu is an Atmega32U4. I tried flashing with atmel flip but now it's stuck in bootloader mode. I'll use the utility linked by exlusive when I get home tonight.
e: QMK Toolbox isn't picking up on the driver. When I ran zadig to install libusb32 drivers the e6v2 wasn't named atmega32u4 or anything, just the following:
The default listing for the E6-V2 drivers is under Universal Serial Bus Devices as 0xC6-V2. I think the only thing I need is to install the correct driver. Then flashing will be easy.
qmk flashing
@amnesia: any tips on flashing the E6-V2 from Round 2? I used your hhkb split layout for mine and flashed with atmel flip but it is now forever in bootloader mode without a proper driver for me to re-flash. Atmel flip simply won't connect to my usb device after pressing the reset button, and qmk toolbox won't recognize any dfu device.