Today when I tried to boot my X299 Dark nothing would come on and I kept getting EE error code on BIOS LED. On suggestion of EVGA Tech Support (thank you Christian!) I switched from BIOS1 (on board chip) to BIOS3 and after that I was able to boot fine (thank God for practice of keeping fallback BIOSes available).
 
Then I switched back to BIOS1 and again got EE on boot confirming it is something about that BIOS.
 
So I used BIOS3 to reflash BIOS1 and after that I was able to boot with BIOS1.
 
Which makes me ask what in the world could corrupt BIOS on chip that was working just fine for weeks prior to this?!

Sultan.of.swing
Did you try and clear CMOS on BIOS 1 before flashing it?

 
I didn’t, this was my first time encountering this error and I was just following advice. Now that you are asking I see this is a first thing I should’ve tried, unstable settings are much more logical explanation for it than corrupted BIOS.
 

Sultan.of.swing
I used to get EE codes on my Dark all the time when RAM overclocking was not stable or uncore offset was too low.

 
‘Uncore’ is CPU memory mesh, correct? If yes I am suspecting it more than my memory itself. Which BIOS settings are related to it, and what values you have them at, please?
 
Also, when it comes to memory I use G.Skill 128GB Ripjaws V kit (F4-3200C16Q-128GVK) running at their XMP Profile (1.35V for 3200MHz CL16-18-18-38). If I later decide to change settings what is the minimum voltage you recommend me trying, in which increments I should be bumping it up, and what is the value I shouldn’t be exceeding for reliable long term 24/7 operations, please? What are your memory settings like, please?
 
P.S. Thank you very much for your help!

MackWage
I have only ever run into this error on my SR-3 when there was a physical problem preventing POST.. such as a memory chip needing to be reseated or a bad connection / short somewhere. 

When Sultan.of.swing commented that this might be due to bad settings I've searched deeper through EVGA forums and found number of others that had same error that went away after they fixed settings. If I had a physical problem it wouldn't have went away and repeated itself just by me changing which BIOS I am booting from.
 
So I a guessing EE error code means anything that is preventing mb from passing POST checks, whether unstable settings or physical issue.

might be a bad flash too. check the hash on the flash file you used.