I have a Cube Orange which currently is stuck with the orange startup LED on but never shows up in the COM Ports. The MicroSD card has a .bin file from ArduCopter 4.1.2 so it was able to be programmed in the past.
Have you verified the USB cable & port communicates properly with other devices? Also try connecting with the SD card removed.
You might need to flash using the SWD port (on the carrier board, with the case removed). We have instructions to do this using J-Link (i.e. EDU Mini) but it can be done with an ST-Link programmer as well.
