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[Solved] I need some help with Supermicro BIOS update.

I'm tying to update the BIOS of my X11SSH-TF motherboard to the 1.0a version. This is the first time I'm doing this with a Supermicro motherboard, I might have missed something trivial.
 
To do the update I'm using a bootable usb with freeDos (created with rufus), with the BIOS files extracted to its root directory.

When it boots I run the "FLASH.BAT X11SSHT6.322" command, the script detects that the FDT is different, as far as I can tell (only a message is printed) successfully generates a new AUTOEXEC.BAT and proceeds to reboot. After rebooting it detects a different FDT for some reason and the script is stuck in this loop...
 
At first I suspected that the usb drive become write protected somehow, but apparently that would result in an unsuccessful AUTOEXEC.BAT generation.
 
Before the update I did reset the BIOS settings to optimized defaults. Some ASUS motherboards require to do this after a new FDT is generated as well, but it didnt help here.
 
Upon inspecting the FLASH.BAT at least I can tell that the flashing procedure didnt start so there is no harm done.
 
Anyone can recommend any further steps I could try to make this work? I dont want to use the recovery mode bios flashing as long as its avoidable.
 
EDIT:
After contacting tech support the following steps solved this problem:

1.      Clear CMOS and boot to DOS

2.      ren fdt.smc fdt.exe

3.      fdt –w 50 00

4.      fdt –w 51 00

5.      fdt –w 52 00

6.      ren fdt.exe fdt.smc

7.      reboot system

8.      back to dos, then run flash.bat X11SSHT6.322 again.

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Why do you want to upgrade the bios? There isn't alot of improvements on the 1.0a version

Desktop: i7-6700K / Asus Z170 S / H100i V2 / LPX 2400Mhz 16GB / 960 EVO 250GB / 2x 860 EVO 500GB / RM750i  / NZXT H440 XB271H + Z22n Monitors

Laptop: Thinkpad T450s / i7-5600U / 12GB / 860 EVO 500GB

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Its a new build so I want everything up to date, also I read somewhere, I cant find it now, officials changelogs would be nice, that it improves M.2 performance, which would be useful as I plan to run freeNAS and put a L2ARC cache there.

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