I have already also posted this in the ROG Asus forums however you loyal awesome EVGA people have always helped in the past with my more troubling PC issues that are hard to solve. I will copy/Paste the same message here and post a link as well. I appreciate any ideas anyone has here. Luckily I can revert back to my X79 system for now until the dust clears. 
https://rog.asus.com/forum/showthread.php?101940-BIOS-POSTS-freezes-detecting-VGA-Any-Ideas&p=719664#post719664

Greetings,
I will try to keep this quick and simple. My Zenith stopped booting today randomly. I powered it on, BIOS speaker chirped once for a POST success. Screen comes on and says, "BIOS is updating LED firmware. Do not shut down or reset the system to prevent system bootup failure." POST code 92. Load VGA BIOS. Stayed that way for several hours to almost 20 hours. 
At this point I powered it down and attempted to clear the message, unplugging everything besides 1 stick of ram, my graphics card, keyboard, mouse and monitor still would bring up this same screen. Swapping my Asus 1080Ti or a NVS 300 resulted in same message.
This message appears before any chance to enter BIOS setup
Clearing CMOS or complete power downs with battery removal fail to clear this message
Attempting a crashfree BIOS 3 procedure fails, even after pressing BIOS button with the Zenith's USB service USB Drive plugged into the BIOS USB Slot. (BOOT LED Lit)
Moved Both Graphics Cards to my old X79 System. Both boot into Windows without any issues. 
POSTing without a Graphics Card will result in BIOS going to detect a HDD/SDD, detects it then beeps at me due to a lack of a VGA. (VGA and BOOT LED Lit).

I am out of ideas and starting to believe it is time for an RMA since I can not interact with the BIOS by any means to even attempt a new flash or BIOS Settings. I moved to my old system for now. Anyone got any ideas? Otherwise I will move straight to a RMA request. I search these forums, and tried several searches on yahoo and google for an answer but no luck. If a related article does exist I do appreciate a point to that direction.

Thank you!

AMD Threadripper 1900X, Asus Zenith Extreme X399, T-Force Nighthawk 3200MHz RAM 2x8GB, nVidia Asus Geforce 1080Ti, EVGA SuperNOVA 1000w T2, Samasung 960 EVO M.2 (BOOT), WD 4TB Caviar Black 256MB Cache HDD (Data).

bob16314
You tried USB BIOS Flashback from a USB flash drive to update to the latest BIOS version?
 
Did it work?..Flashback button start blinking, then stop blinking?

Flash Back (CrashFree) would never start even with the "Support Flashdrive" plugged into the BIOS USB Port on the motherboard. 

bob16314
USB BIOS Flashback has to work, just has to.
 
The latest BIOS Version 1003 is named ROG-ZENITH-EXTREME-ASUS-1003.CAP..Rename it to ZE.CAP and put it on an empty USB flash drive..Put the flash drive in the USB BIOS Flashback port (5), press and hold the USB BIOS Flashback button (7) for three seconds/until it starts blinking (meaning it's flashing), wait untill it stops blinking (meaning it's done flashing)..Remove the flash drive..Boot up, hopefully.
 
Use Flashback with your box just plugged in, not booted up.

Use the ASUS BIOS Renamer for USB BIOS Flashback Tool to rename the BIOS
1. Download the tool here from ASUS and extract the .zip folder
2. Put the ROG-ZENITH-EXTREME-ASUS-1003.CAP BIOS file in the same folder as the BIOS renamer tool
3. Run the renamer tool
4. Use newly renamed BIOS file (ZE.CAP) for USB BIOS Flash back.
 
I have to rename my BIOS for it to flash..Unless things have changed, you may also have to do that too.
 

I just attempt again and BIOS Flashback will not respond. I can hold that button for three second, or 5 minutes. Nothing happens except the board freezes. I took quick video hoping I could upload a small video here but no luck lol. The last thing I could try is buying a very small USB drive that is different from the Support USB Drive Asus sent but since I can not even get the button to light up at all. I do not think it would work

bob16314
I'd try another stick, or format the one you have..I've used both an 8GB Lexar and 64GB Kingston stick formatted to FAT32 (which it needs to be) and USB BIOS Flashback works fine here after renaming the BIOS file. 

I threw a old one in just to see if it would respond after pressing the button but it does not respond or the USB stick shows any sign of being accessed. I will dump the contents of my old USB drive and prep it. ill answer back in hopefully 20 mins. 

bob16314
Rufus works perfect here for formatting and other things, I use it fairly frequently, my "Go-to" tool for USB flash drives..Choose FAT32 for the File System and only checkmark the "Quick format" option..Good luck.

So I tried twice, using Windows format Fat32 and Refus. I also attempted all USB ports one at a time. BIOS Flashback never responds or does the activity LED on the USB Flashdrive. Everytime I push and hold BIOS flashback it seems to freeze the board where CMOS, power and reset stop responding.

New Build or New Issue ?
 
remove power, pull the MB from the case - test on non-conductive surface (wood or clean cardboard will work)
 
confirm all power cords / connectors are fully seated (CPU/EPS and 24 pin)
 
CPU cooler overly tight or tightened unevenly ?  may have to check for bent pins under the CPU

This is an old thread, but just in case someone finds this, I had the exact same issue.
I removed all but one RAM stick, GPU.. nothing. Tried to use the USB flashing feature, the board froze, no flashing in the BIOS button. Power/Reset buttons didn't function, nothing. Had to do hard restart by cutting power to PSU.
 
Anyway, I ended up removing the CPU and what do you know.. the flashing feature works as intended! There I was for a minute thinking my hours of troubleshooting had come to a successful end. I reinstalled CPU and the problems resumed, great.
 
So I took my motherboard to the vendor I bought it from and turned out that one, a single damned pin in the socket was bent!!!! I sure as hell didn't drop anything there. I kept the covers on the socket until I started installing the CPU (2950X).
And boy is the installation of the CPU a mayor pain.. getting the top screw to thread is a serious test of patience. I hate that socket so so much.