Exactly the same thing here. I tried to update to F6, but it failed on the main BIOS, and can only boot from the secondary BIOS now. I actually need the newest X02 BIOS as I'm running phase change cooling and have a bit of an issue with the cold boot bug, but don't want to update the secondary F3 BIOS the board shipped with in case I brick that too.
Is there some mechanism of updating the primary BIOS only? All help much appreciated.