For modified BIOS you have to flash a certain way, using AFU or AI Suite, or USB Flashback - [Guide] How to flash a modded AMI UEFI BIOS
For the mod BIOS, in this instance and for quick and easy way, I would flash the stock BIOS in there first, then flash again using AFU and /P switch only, that is all you need from the mod BIOS.
AFU works with cap file, not modified one, use /CAPSULE Switch. If you want to remove the capsule for easier flashing, open in UEFITool and right click the first section shown in the middle (AMI Aptio Capsule) and choose extract body, this is your BIOS rom 2KB smaller than the cap file.
Or, since this is backup spare BIOS, just flash stock BIOS into the chip using EZ Flash, youād be done by now 
. And yes, EZ Flash works fine with .cap BIOS, just not modified one in many instances.
Your NVME insert is OK!
Hi, thx again for the quick answer.
Please donāt link to this guide, itās not helpful for the case that flashback is not working.
So if I understand you correct, I shall:
1) start with the original BIOS
2) Convert my cap file according to your description (This part is missing the guide!!!)
3) program the bin file with afudos and parameter /P only.
Typo corrected
Correct?
Flashback works, you just need to find compatible USB stick. AFU works as well, as does AI Suite method.
Yes, but use /p switch not /b
ARRRRRGHHH
OK, I managed to make a hotflash of the destroyed Bios chip, so I now have to working chips with ASUS original Bios 2501, fine.
I canāt do flashback, all my sticks are not compatible as it seems.
Good, I created a file ābios.romā with UEFITool following your description, and yes its file size is 2 kByte less.
Good, I made a bootable USB stick with FreeDos, put afudos.exe and bios.rom it the start:
afudos bios.rom /P
I get something like (I wrote it on paper, obviously I could not use cut and paste)
AMI Firmware Update Utility v3.07.1
Reading flash ā¦ done
FFS checksums ā¦ ok
1e - Error: Secure function is not supported on this file.
How can I program my bloody modified Bios?
OK, I made more tries:
Here in the forum an older version of afudos is linked, which support /GAN
I made several tries, and finally I did not get ANY error messages, when I used:
afudos bios.rom /GAN.
Horray, I programmed the mod. bios, or not?
I do not see any difference now, I hoped I have a possibilty to choose the SSD as boot device.
It does not show up. What would be the expected behaviour?
How can I check the I really programmed the new BIOS?
The NVM SSD (Intel 600p) is fully usable under Windows 10, but that worked before, too ā¦
Great job!! One day you will find USB Stick that works with your USB Flashback!
Yes, when you used /GAN it flashed, I assume, no errors correct and it showed āUpdating Progressā (reading, erasing, flashing) correct? To verify if your mod BIOS is on the board BIOS, make a dump from the chip, then open that file in UEFITool and see if your mod change is there or not.
To make bootable NVME you have to follow the guides on how to set that up, usually you cannot see it how you would expect to be seeing it look in the BIOS (I think it shows as PATA or something odd/unexpected). Check the guides on that, itās all explained.
If you could always see NVME in windows with this motherboard, BIOS mod is not required at all, and should not be done since BIOS is already made NVME compatible from the manufacturer.
Hi again, unfortunately it was all in vain:
afudos with /GAN writes out erasing ā¦ programming ALL, no error messages, but then nothing is programmed.
I rebooted, started again afudos, save bios with option /O. Then I rebooted again to Windows and compared my modified file with the save file, the NVM module was missing.
I could not believe it, programmed the BIOS 3 times, NOTHING.
So now itās clear why I did not see any change in the BIOS, there was none.
I have read now all the postings in the thread, and it confirms my finding: when you have a security protected Bios, you canāt program it with Afudos, it simply does not work.
I also tried the AI-Suite trick, itās actually very simple: Before starting the real upgrade, you replace the original Asus Bios with your modified Bios. And it starts programming.
After 2 minutes it was finihed and it suggested a re-boot, I did, booted to FreeDos, saved bios, booted to Windows, checked the save Bios with UEFITool => NVMe module missing again :-((((
So same behaviour as with afudos /GAN, it takes some time, pretends to do something, but no change to the Bios.
Now I understand why CodeRush wrote : Afudos does not work, get a programmer.
Try next version that supports /GAN - I sent you PM correct with several DOS and a windows version? If it was Intel I could help you flash with FPT, but yes if you cannot get it with AFU you will need programmer.
And, aside from all these reasons, everyone/anyone looking at any Mod BIOS should pickup programmer first just in case, they are only $3 or $6-7 if you need cable too.
Did the package I sent you contain wAsusFU? If not, I will send, not sure if it will work on your board but we can try.
Hi,
You did not send me anything.
I used the latest AFU (downloaded from AMI) which included Windows, DOS, ā¦ afudos was version V3.07.01. *** EDIT That version has no /GAN support ***
For my tries with /GAN, I used afudos.exe (downloaded here from this thread) it is version V3.06.01.
The mainboard is Asus M5A99X EVO R2.0 it is an AMD AM3+ board, with AMD chipset.
Please send me something, that works 
Sorry, I thought I sent to you! PM Sent
Hi,
Thx, I tried all of those tools, none did change something in my bios (the Tool for Intel Chipsets and the older afudos version give an error)
Afuwin and afudos with /GAN tell that everything is erased and programmed, in fact nothing is done. Also the programming is way too fast, so it definetely not working.
I will try some more smaller USB sticks and give flashback again a try. I donāt expect much, because my 2 GB stick formatted with FAT32 is not accessed at all by flashback, when you try to read something from the stick under Windows you see a red light, The stick is quite slow, so it is easy to see. There is no right led on the USB stick during flashback procedure, itās the same with all my other USB sticks.
Also tried just for fun a 500GB USB 2.0 harddisk, with USB flashback, it is simply not powered up (There are white leds that glow when the harddisk has power).
The wAsusFU did not work either? GAN is not necessary always with that, but can also be used there too.
Flashback works, and works well, but you have to find compatible USB stick. Usually smaller/cheaper is better, sometimes 128Mb-512MB work better than 1-2GB, above 2GB you have to get really lucky for that to work
Flashback with HDD USB probably never work, even if you powered the HDD with another system, due to compatibility with normal USB Sticks is hard to find sometimes I doubt it would ever work with USB HDD
Both chips now programmed and working anyway, correct? I assume so since one of your later posts you said you finally hot swap flashed it, maybe only a waste of time to keep trying until you get more cheap USB sticks (Order a bunch of different 99 cent ones on ebay)
Or just order $3 CH341A flash programmer from ebay and never have to worry about any of this again.
Yes wAsusFU does not work either, it gives something like:
>wAsusFUX64.exe 99xevor2.CAP /P /B /K
======== ASUS Flash Utility Ver 1.13 for WinPEX64 ========
2018-10-09 17:19:28
Get Flash Information : PASS
Get Rom Layout from Rom : FvReadFileNonCompressFromRom Failed
FAIL
2018-10-09 17:19:30
Return 255
You are right, I stop trying to flash it with software, so I try with some usb-sticks from friends, will try with a 512MB and a 256MB stick, letās see
Yes, without programmer, best thing to do is find a compatible USB flash drive. That way youāre not forcing anything to be flashed incorrectly.
Hi again,
I already got the 512MB stick, no chance to do a flashback. I formatted it with FAT32, put my modified 99XEVOR2.CAP on it.
The flashback LED on the mainboard flashes several times, and then lights permanently.
I alreday wrote it, I think flashback is simply not working on my board, because the stick is not accessed (when you read from the stick the led on the stick is on). Also could be that the Flashback USB port on the mainbaord has a problem.
I will also try the 256MB, but I donāt believe something will change.
So I shall go and buy a programmer. I do not like this option, because I am sure, that I will use it only this single time, so itās weird to order something from China, ā¦
What CH341A do you recommend?
Or maybe I let it program again and order a chip, thatās 14.50 EUR incl. shipping, then I have 3 Bios chips for this mainboard, lol
That means USB not compatible, or no BIOS found on the drive. Is the BIOS in the root of the USB, not in any folder?
Sometimes you have to try lots of USB, I went through a pile one day for one board, then next time I needed it all those worked on a different board, so itās all up to what USB compatibility is programmed into the BIOS/board already.
Flash programmer only costs $2.50 on ebay, purchase there so you donāt feel like you are wasting money. Donāt feel weird buying cheap things from China, I purchase cheap crap there all the time, sometimes even items costing $0.50 to $1 shipped by themselves, I donāt know how they do it and make money, but I get the items eventually.
You might get lucky and only need this one time, but I doubt it, since you want modified BIOS you may find it useful all the time, plus you will never have to worry about bad BIOS flash again youāll always be able to fix if a flash goes wrong.
I recommend any of the $2.50-3.00 ones on ebay. You have two working chips now, no need to order a third? Yes lol 
If you want to pay more $$ and get a kit with cables, that you can use on other boards where BIOS might be soldered to the board, you can get cheap kit like EZP2010 or EZP2013
Yes, only one file was on the stick, no folders. Stick is not read.
You wrote "so itās all up to what USB compatibility is programmed into the BIOS/board already."
The existing Bios canāt have to do with it, or is the Arm processor using the Bios??? The Bios is for the x86 CPU only. The USB flashback thingy shall work without CPU, RAM, ā¦ Well I cannot really tell, because I have never seen it working 
I am going to order the programmer now.
I have only seen USB Flashback work without CPU on modern Intel based boards, I do not know if it works that way on older Intel or AMD Boards, CPU may or may not need to be installed, but the process has nothing to do with using the CPU.
Flashback is part of the BIOS, and any/all compatibility built into it is either stored in the BIOS itself and or another chip on the board.
Once your programmer arrives all your headaches will be solvedā¦ Which I assumed already were since you have two working BIOS chips now?
Hi,
OK, I received the programmer today, I ordered one with an USB cable.
Can you help me to get it running?
I installed some drivers (I am using Windows 10 x64), but I guess the driver installation is not correct.
When I start "CH341A programmer" or "CH341A programm v1.29", both programmers say No device connected.
Do I need to enter a chip before I start the program?
There are 3 possibilities to enter the chip: One from the first program, second possibility from the 2nd program, 3rd possibility what is printed on the boardā¦
Also there is a Dip Switch 5V or 3.3V, which is right?
Hi again, actually posting this picture was a very good idea :DDD
Both Dip switches were set into the other position, so 5V and TTL. 3.3V and the chinese character (like in the picture!) worked better, the programmer got recognizedā¦
I flashed the chip, now testing 