I got one issue here:
I have GTX 1080 SLIx2 (one monitor connects to it, via DVI) and a GTX 645 (two monitors connect to it, via HDMI and DVI). MB is ASUS X99-E WS USB3.1, it has PLX chip, so video cards connect to PLX, not directly connect to CPU or PCH... then, I run bios updater, cmd window showed up with logging like "detecting adopters, balabala, found PLX, balabala ", then one monitor @ 1080 and one monitor @ 645 went black. I waited for minutes, and I had to reboot the machine...
I guess VGA driver caused it?