Well, I doubt that this is true. The lat/long for the WTC is hardly a secret. I can still get it right off of the Internet or MS Streets. Why pull all of the "games" to change an item that anyone can find. Has anyone else heard this story and can confirm or deny?
And your proof is?
The point is not that they got simple long/lat numbers from the game. The point is that they could do the actual run from Boston to New York using the game and make notes of the several changes in altitude and long/lat needed to plow into the WTC. My flight school got this info from the FBI when they were going through their records. Check with Microsoft and you will see that there was a recall in September.