No it is not possible to backup the flash with the original firmware loaded. As you have found the original firmware does not appear as a com port. This is normal, openGD77 uses different drivers. However loading OpenGD77 does not change any of the calibration or flash settings so a backup immediately after upgrading the firmware is worth doing.
It is possible to go back to the stock firmware using the standard stock firmware sgl file and loader.
Colin.