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.
All that I have read about Flight Simulator is that MS delayed the release of 2002 because of sensitivities related to the attack. They also issued a patch for 2000 that removed the towers from the NYC skyline. I have read nothing that indicates that MS changed the lat/long in any of the sims or recalled games.