There are numerous examples of aftermarket ATX & E-ATX form-factor motherboards swapped into Area-51 R2 the past 5 years, I've yet to hear of an owner complaint that a new motherboard couldn't be installed & work, except yours today.

I've also been upset in the past discovering small things done to encourage people into buying a newer model versus upgrading.   

But in fairness to Dell, I think for most people upgradeability refers to ram, gpu, hard drive, ssds, fans, aios, coolers, pcie cards, stuff that is designed for easy plug and play swap.  If you change the motherboard, that isn't even an upgrade, that's not even an Alienware anymore. That's an custom pc in a Dell case. No prebuilt manufacturer is going to extend their warranty to a third party motherboards like that. 

I mean it's cool if that's what you want to do, I think the custom 51 alx pcs look nice and admire the work that goes into retrofitting vintage models. You just need to be able to figure it out on your own like any other pc built from scratch and be prepared to work with and troubleshoot any Dell proprietary issues. 

Yeah, I 've only read about 2 upgraded mobos for my model. The problems that arouse through both makes it not worth it to me. I have a Intel I7 6800 hz cpu, I don't do AMD. Yeah i put it on Craigslist today to sell for parts. 

1. But in fairness to Dell, I think for most people upgradeability refers to ram, gpu, hard drive, ssds, fans, aios, coolers, pcie cards, stuff that is designed for easy plug and play swap.

2. If you change the motherboard, that isn't even an upgrade, that's not even an Alienware anymore.

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1. Agreed

2. Exactly. 

I have windows 10 pro via the windows insider program. No key needed.

As far as the damaged motherboard - it was tested and a power surge wrecked the motherboard.

I took it to 3 pc repair shops trying to get it repaired.

PC Component did the final repair. I was told that it was the power surge that damaged the motherboard. Nobody wanted to just replace the bios battery bowl.

1. I have the Alienware Area 51-R2 (10 core) and broke the BIOS battery bowl (plastic) and damaged the motherboard when trying to change the bios battery.

2. The sad thing is that the Command Center is NOT compatible with  a non-Alienware motherboard. So therefore no lights !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

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1. A technician or electronics hobbyist could have fixed that for you (soldered-in a new one) for a couple hours labor. Yeah, some of this stuff is old and fragile. 

2. It doesn't even have a connector for the LEDs (only a real Alienware MB has the MIO-Board circuit). Maybe also some fans, but I'm sure the shop re-wired those for you.

At least you got it back into service.

Were you able to retrieve your Windows 7/8 key for free Windows-10 upgrade ?

I have the Alienware Area 51-R2 (10 core) and broke the BIOS  battery bowl  (plastic) and damaged the motherboard when trying to change the bios battery. Almost impossible to get the stock motherboard!!!!! Maybe a used one if lucky!!!

A pc repair shop put in an ASUS X99 Deluxe II motherboard for $514.

It works  BUT:

The sad thing is that the Command Center is NOT compatable with  a non-Alienware motherboard.

So therefore no lights !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Install Command Center A51 R1-R7 | uTube

I tried that link yesterday and thought it was going to work but then got an error message.

Tried several times and no luck. 

Re: Command Center is NOT compatible with  a non-Alienware motherboard.

It doesn't have a “connector for the LEDs” (“only a real Alienware MB has the MIO-Board circuit”).

From personal experience and other users experiences: 

Command Center is compatible with many non-Alienware motherboard.

Neither Alienware nor Non-Alienware motherboard in Area 51 have proprietary connectors for the LEDs.  (whereas in Aurora R5-R8, it is true that only Alienware motherboard has proprietary connectors for LED)

New Area 51 R2 motherboard (does not have to be X99) communicates with AW FIO board via two cables: front panel power cable and USB1 cable.  If both are connected correctly, you should first test LED using AlienFX tester.

For easy swap, new motherboard needs to have industry standard 9 pin front panel and 9 pin usb2.0 header.  ASUS motherboard does not use standard 9 pin front panel in contrast to MSI, EVGA, Gigabyte board. not sure how your ASUS is wired, but you must have all 9 pin rewired correctly.

https://www.dell.com/community/Alienware-Desktops/Area-51-R1-front-panel-10-1-USB-to-ASUS-20-8-panel-pin/td-p/7467551

the LED are controlled by FIO and logo board.  FIO communicates with mobo via the two cables.  Logo board is controlled by FIO.

This is what you want to see running AlienFX tester, a small app inside AWCC folder).

ASUS 20-8 pin front panel

You need to make sure all 8 pins including (2 pin each):

1. PWR SW,
2. Reset,
3. HDD/IDE LED,
4. Pwr LED

are rewired correctly from Alienware FIO 9 pin to ASUS 20-8.  Pin 9 is NC.

The rear FIO AlienFX board is a simple USB device: it needs 4pin Molex power & the double-ended internal USB2.0 comm cable connected to itself @USB1 header & the other end to a motherboard USB2.0 header

If we pretend the original internal USB cable (& FrontPanel1 cable) are very short cables (~10inches), it is almost always certain you will need to buy an internal USB cable extension (male prongs) fpr it, or, buy a new longer basic (9-wire) internal USB cable of 22" - 24" to reach new mthbrd USB2.0 header (the same is true for the Front Panel cable: extend it or buy a new longer one), see here post 41 My experience upgrading an Area-51 R2 to 2020 specs

No external LED lights, 'no instance of an object' error in CmndCntr, 'no board detected' when launching AlienFXTester.exe, or other errors may indicate FIO board has no 4pin power or the USB cable isnt connected or both

You said you had no lights, then you said you have a 'thermal error', which is it?

I might try the newest CmndCntr version 4.8.25

If FIO has power & USB cable is connected to its USB1 header & also to a mthrbrd 2.0 header, & if lights work (the real issue here) but it throws errors, I might uninstall & roll back to an earlier version 4.0.59 or 4.0.38 (uninstall then reinstall in Windows7 Compatibility Mode &/or Win8.1 Mode if it acts 'weird' in Win10)

Note that the Area-51 R2-R7 models have a built-in 'flaw', such that when trading out the mthrbrd for a typical aftermarket type (Asus/MSI/AsRock/Giga etc), one of three things can happen: all lights work > front lights work but side panels fail to light up > no lights work > there is no cure for when side panels or no panels light up, it seems to be based on the exact mthrbrd u chose & only recently did someone start a 'registry' or list for known good boards where all lights work ie true compatibility Motherboard Swap Database

Here the Asus Rampage x99 allowed lights to work: Tutorial Upgrade 51 R2 with X99 Mainboard 

Not many owners who swapped their mthrbrd still visit here, & I havent owned an R2 in years, maybe start a post at AlienOwners, see if anyone has ideas

If your FIO has power & USB connected, you should get at least one exterior LED to light up, if so then the hardware works & if what's left is a thermal control error when u launch CmndCntr, I cant help with that other than have all your drivers updated, OS updated, uninstall AWCC & reinstall

Asus Sabertooth x99 also worked 51-R2 1080 SLI Hybrid 6850K ASUS Sabertooth X99 Performance Build

Re: one of three things can happen: all lights work > front lights work but side panels fail to light up > no lights work > there is no cure for when side panels or no panels light up, it seems to be based on the exact mthrbrd u chose

It is quite possible that when it is scenario 3 (no lights), user did not connect the usb2.0 cable and front panel cable correctly.  This is assuming all case lights worked before the motherboard swap.  If it is scenario 2, it may be due to the new motherboard having a constant 5Vsb connected to usb 2.0 header when system is off and power connected.

if I am not mistaken, when R2 case houses a genuine Alienware R2 motherboard, there should be no light on (including power button alienhead) when system is off and connected to power.

incidentally, one does not need a working Alienware motherboard for all lights to turn on.  Actually as one eBay seller of R2 case showed that one does not even need a cpu. An alien motherboard without cpu can still turn on all the lights.

Took pc back to repair shop.

Gave them the link for used Aleinware MB.

ASUS MB not working with Aleinware command center software so light not working !!!!

I do not have the knowlege to install a MB.

Spent $650 so far and not  working right !!!!!!!!!!!!!!!!!!