I encountered an issue with Flashing the bios from usb pen.
It turned out to actually not be related to the method of flashing with usb but rather than during the process I had dumped some files in the root of the factory formatted DATA partition.
One of them files was startup.nsh script and this was causing UEFI EFI Shell: Cannot read from file - 800000000000001F every time i tried to boot into UEFI EFI Shell, regardless of whether I had the USB drive in or out of the machine.
Thanks to @joshwiththegoodhair for resolving this problem. I have kept all the posts and moved them into this thread incase it is useful for someone else in the future.