I had the same issue a week ago when the flash failed and I got the 3 red led and middle fan stuck at 100%. I had to close out every application in the task bar like origin, steam and so on. Then it finally the flash worked. The saying it is just a 2980Ti was the result of the latest version of X1 Precision.

So I followed suggestions I found in other threads and this thread to disable all TSR's and update the firmware right after a fresh boot. 
 
1. I disabled Corsair Link, Mouse/Keyboard drivers from loading on startup.
2. I did a fresh boot and then disabled Bitdefender AV and closed all TSR's.
3. I flashed with 2080Ti_FTW3_E202 and it ran then closed automatically.
4. I started EVGA Precision X1 3.10 and it prompted me to flash my firmware and I did so successfully.
5. My middle fan stopped spinning at max and Precision X1 3.10 showed 3 fans instead of two.
6. Since I closed a bunch of necessary drivers I did a full shutdown of my PC and disconnected all power.
7. I started up my PC and my middle fan seemed quiet. In Windows I started Precision X1, there was a long pause and then my middle fan spun up to max again and Precision X1 showed two fans again.
8. I repeated the above steps to disable Corsair Link and mouse keyboard drivers, did a fresh boot and closed all remaining TSR's.
9. I ran the flash again and it flashed, then I opened Precision X1 3.10 and it updated firmware successfully again.
10. I restarted my PC without a full system shutdown and let everything load back up and Precision X1 shows 3 fans, my card is quiet and everything seems ok.
11. I added EVGA Precision X1 as exclusions to my BitDefender AV. Note: EVGA Precision X1 is in '\Program Files' and LED sync is in '\Program Files(x86).
 
I will monitor and continue to update if the card remains stable or if I have to keep re-flashing it.
 
 

 
Yes, I flashed successfully after the 'fresh boot-disable all TSR's Tip' then I did a full shutdown, my middle fan was quiet and not sped up to the max speed. When I re-started Precision X1 there was a long pause, then my middle fan spun up to max again. Precision X1 3.10 showed two fans only again. I went through the process again and re-flashed but only restarted my Windows to re-load all my TSR's and everything is good.

This is still not resolved. After I get the MCU update and firmware working if I remove ATX power on shutdown the middle fan will speed up to 100% again at startup and I have to go through the process of applying the MCU update and firmware again.

Update:
 
-I've spent the last 24 hours troubleshooting my '100% middle fan speed/2 fans only recognized' issue and this is what I've found:
 
1. I no longer think I am losing my MCU update or firmware when I do a full shutdown. It seems to be a mainboard compatibility issue possibly due to my PCI set to UEFI.
2. The card works in my Son's PC fine. It has an EVGA x79 mainboard set to Legacy.  The fans are quiet at first boot and Precision X1 3.11 sees all 3 fans. I can do a full shutdown removing ATX power and the card still works normally. We both have the exact same Corsair Case.
3. In my system with an EVGA x99 FTW K mainboard set to 'UEFI PCI' due to my using an M.2 drive. I have the middle fan at 100% issue and Precision X1 only sees 2 fans.
4. I can quiet my card down and get Precision X1 to see all 3 fans by going through a strange process of booting into my bios and then powering off with the power button and holding it down for 15 seconds and then re-start up my PC only with the power button. Sometimes it takes a few tries. When I can boot and my fans are quiet, then Precision X1 sees all 3 fans and my card runs normally. Every time I do a full shutdown by removing ATX power I need to go through the process again. 
5. I swapped out my EVGA 1000W Power Supply with an EVGA 1600W T2 including all the cables and this didn't help.
6. I flashed my X99 FTW K with the latest bios and this didn't help.
7. I moved my card to the other X16 PCIe slot and this didn't help.
8. I think it may have something to do with my bios being in UEFI boot mode and PCI in UEFI ROM mode but I don't know for sure.
9. Next thing I will try is setting my bios back to Legacy and seeing if that helps but I'm tired of working on it for now and when I switch from UEFI to Legacy I always end up with a big mess getting everything to work again.