I had a similar problem myself with an older PC... and yes, it simply denied the existence of the HDD. I was able to use a command prompt to manually copy various registry files from my system restore, which seemed to work. You've probably already tried that, and I guess if the BIOS isn't recognising the device, it probably won't like it in DOS either
Edit: BTW, did you try flashing the BIOS? Obviously that might be difficult if it's a DELL or HP or whatnot, but perhaps refreshing the BIOS might force the HDD detection
I have not tried updating the BIOS, might be something to think about.