So I messed up during updating the bios. I think I might have interrupted the first long reboot some way. Currently it boots into the bios setup interface. I can change settings and it saves it. But it never goes to booting the disk. It always goes into the bios setup. I was able to boot into the uefi shell and flash the bios again. The flashing script completes, but it seems whatever is supposed to happen during the long reboot, is not happening. It just goes back to the bios setup. It is Udoo Bolt v8 btw. Do I still have options? I have an Arduino that I can reprogram into an SPI (possibly JTAG) programmer. Can I flash the bios that way? Can I buy a new bios chip and solder it in by hand?
I could be wrong but I believe the "Long Reboot" after the BIOS flashing is dumping some sort of extra firmware into the Embedded Controller of the Bolt, it has nothing to do with booting operating systems, the SATA and NVME (PCIe Lanes) are part of the CPU and not the EC. Check your booting compatibility options like UEFI or Legacy. Also I would suggest Load Defaults at the BIOS after flashing.
Isn't the flashing utility doing a verification pass on each of the Blocks it writes? The PDF inside the archive does show this might be the case, so if the utility did not display any sort of errors to you, everything should be good.