A few things here. NEVER flash bios from within windows. Always use a USB formatted in fat32 and do it from bios menu.
There is a special place to enter questions about x99 boards might want to post there also.
http://forum.giga-byte.co.uk/index.php?board=58.0Method #1:
1. Shut your PC down (if you're reading this guide, than your PC isn't working anyways)
2. Hold the power button until the PC starts and shuts down again
3. Press the power button again, your backup BIOS should kick in now and should re-flash the main BIOS if there's anything wrong with it.
Method #2:
1. Shut your PC down
2. Hold the power AND the reset button for about 10 sec, than release.
3. Backup BIOS should kick in anytime soon now.
Method #3:
Had to use this one in order to get my 990FXA-D3 working again. Backup BIOS kicked in using method #2, but I was back to the good ol' no signal state once the procedure finished..
1. Short out pins 1 and 6 on the main BIOS chip (pin #1 should be marked with a red dot or whatever)
2. Tell a friend (or a relative) of yours to press the power on button
3. Remove the ghetto-like jumper you're holding between pins 1 and 6 as soon as you hear a beep.
4. Backup BIOS should kick in again and everything will (hopefully) be fine.