With all the drives removed, I booted off of an Acronis Boot CD (via USB DVDRW drive) and saved the image of the onboard flash to another USB stick.

Can you elaborate? If I can get GRUB/LILO to boot some sort of Linux from a flash drive I can probably format the onboard flash NTFS/FAT32 and unbrick mine.

I hoped it could be this easier... but the problem is when the real BIOS is gone, or just not used as in the case with the recovery BootBlock BIOS, Linux nor BSD nor DOS sees any of the hardware on the machine.
Linux for example detected some hardware on the PCI bus, but was unable to setup it properly because of missing IRQ routing information, etc.

You may be able to use this to flash a new BIOS that does not include the USB check, though I have not tried this (ymboc is the BIOS expert, I believe) and you would lose your current BIOS/serial number that authenticates your WHS (though you should be able to activate with the product key on the bottom of your server).

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Alex Kuretz
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The strange thing is that I wasn't even able to make awdflash work under recovery BIOS. Maybe I need a special version for this recovery mode, or I'm missing some command line switch. I have tried only to backup my BIOS though, but always complained (I've posted in previous posts about it)
As for the serial number and WHS, I don't really care about it because I don't plan on running it when I get my machine up again

Weird, I thought most modern OSes tended to ignore the BIOS in favor of their own IO routines once they got into pmode.

I think they need the BIOS or at least the ACPI table to work properly.

I'm a dabbler with bios's... I can do some basic assembly but it was all mickey-mouse school assignment useless stuff... wouldn't know where to begin to fix the limitations in the bios.

However I was thinking... what would happen if we grounded the USB +D & -D pins on the onboard flash chip (not the actual memory chip, but rather the usb<->flash chip)...

A friend of mine gave me the same idea, and I've just downloaded the samsung flash chip datasheet.
He also told me that some flash chips, used in home routers have a special pin that clears the whole flash, I think I'm going to try this later today and let you know how it goes.

I'm not sure but I think the samsung chip is just the memory... I think (but haven't confirmed) that the USB<->flash chip is the ICS chip closer to the CPU.

Yes, you are right, the Samsung K9F2G08UXA(at least on my unit) is the flash memory.
I'll try to investigate the other one this weekend... because I had no luck so far in finding shop with the rework equipment capable of desoldering the BIOS chip and soldering a socket.

Re: trying to find a quality place to solder a Bios socket... The place I went to was a little shop that is the factory warranty authorized repair shop for a whole bunch of electronics manufacturers for my area (panasonic, samsung, pioneer, etc etc)... I found them in the yellow pages under electronics repair (their ad marketed that they repaired plasmas)... basically I called everyone in the yellow pages and asked if they did Surface Mount Soldering.

The ICS chip near the CPU seems to be the clock generator. The real USB<->Flash bridge chip is located on the other side of the board, exactly under the Samsung flash chip, a SMI SM3210F chip. So far I'm unable to find datasheet for it, but I'm continuing to search.

Argh... good catch. I was reviewing all my pictures (both sides of the board) the other day... and sure enough when I check today there it is right where you said it was... can't believe I missed it... bah!

You've probably already found it but for the others watching:SM321 Product Info

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Looking at the attached picture... maybe temporarily disconnecting/grounding the 12Mhz Clock might be enough. There's some other interesting looking stuff going on but electronics is not my background so I can't decipher much.

It worked! Shorting the data pins on the SM321 chip did the trick, I was able to boot FreeBSD again, and restored the Flash contents, and now my ex470 is UnBricked!