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.
Sorry, I guess I'm overly sensitive today because I posted something yesterday and got visciously attacked (it ended up what posted was not accurate).
I have a lesson tommorrow, I'll check with my flight instructor for details.
On a related point, the instuctor told me that a 16 year old kid came in for lessons and knew all the approaches to the local airports and landmarks from the air before taking off. He had flown the area so often with Flight Simulator that he had memorized everything!