Hello,
What I am about to suggest is to be taken with a grain of salt, and I cannot be liable if any damage happens to you or your computer. In effect, you will be performing a hardware hack.
The components that work after a lightning strike themselves are rather astonishing. I would not bet the house on them working for a length of time, as if lightning can over come 3 million volts per meter (the resistance of air before it sparks), then what chance does a small IC chip have of survival? I hope it works out, but if it was me making the purchase, I would have walked by.
Anyways, the motherboard might be looking for a voltage drop across the fan circuit, meaning it could be simply looking to see if current is flowing (the fan is turning, using electricity), and if there is no flow, there is no go. Or, it could be smarter looking for precise measurements for the fan. It might even regulate the speed of the fan based on the heat, and you might later discover that if the circuit thinks the computer is getting too warm, it will proactively shut down on you.
As a hardware hack, you have two choices:
1) See if you can move the fan from one case to the other. Mount it somewhere so it does some good, but have a fan there, maybe blowing the same direction as other fans. Do not have this fan blow against another fan though because it might cause a stalemate in the air exchange, and cause a burn out condition.
2) Measure the resistance of a comptuer fan, and go to Radio Shack, and get a resister to place across the jumpers. The resister will use electricity, and make a little bit of heat, just like a fan would. You might want to use a variable resister, so that if you have to tweak it a bit, you have some leeway.
Either case is risky, and should be considered last-ditch efforts. Anything that you do could burn something else out, or cause other problems. It is up to you on how bold you might want to get.
Christian