If Gigabyte said to RMA I guess it's toast. But this was exactly the entire point of what dual BIOS is supposed to prevent. Flashing one BIOS shouldn't affect the backup BIOS.
Did you try booting with just a single memory module and swapping them? I can't believe the backup BIOS wouldn't work unless you somehow saved a bad settings config to it and needed to clear both? I don't even remember how that works, but it's a lengthy process just to flash the backup BIOS. I'd really like to know what happened, because this defeats the purpose of buying hardware with a backup BIOS entirely.
Yes, I tried single ram and swapping them, as well as no ram and attempted again on the slot at the other end just incase the ram slots were installed backwards. I can only guess now, but it seems like the restart after the bios update somehow falsely read as a successful boot and which caused it to back up the bad bios. Not sure how since it didn't seem to get anywhere near posting but can't see any other logical cause. The board was also just confirmed bad by Amazon return department, thankfully; otherwise they had planned to deduct 15% from my return if they found fault was physical defect caused by user negligence.