There is radar tracking data corresponding to all four aircraft. However, Flight 93 in specific did pass briefly through a radar "dead zone" (I think it's the only one, but I'd have to hunt to be sure; I haven't looked into this in depth), and theoretically it might have been possible to pull a "switch." However, the depth of coordination, planning, and dumb luck required for this to have a chance of success would be extraordinary, and I don't see how this would fit into any conspiracy's plans in the first place.
R.Mackey, I want to acknowledge what you're doing here, and also those people engaging with you as the OP requests. I have simply read this thread thus far, wanting to respect the intent of the OP, and not having any questions to pose myself at this time.
However, I hope you will not mind if I step in here as I think I can contribute to this point.
To refresh, the original question, from 1337m4n was:
Is there air traffic control confirmation of where and when the four planes crashed?
Air Traffic Control confirmation can come in three distinct ways. The first of these is radar data, which tracks aircraft. A "chain of custody" of sorts for the radar return would need to be established - from the point prior to hijacking, following the same return through the system until the moment of impact.
The second is eyewitness confirmation. Air Traffic Controllers are of course in constant radio communication with a multitude of pilots in many different aircraft. Those aircraft have windows, and those pilots have eyes. If a pilot witnesses the crash of an aircraft this can serve as evidence. Again, a sort of "chain of custody" would need to be established to demonstrate the aircraft was watched at all times.
The third is via the airlines. Each of the airlines has their own system for monitoring and tracking their fleet, and this data would provide evidence of the aircraft's flight and eventual fate. The same rules of "chain of custody" apply.
Now, the problem here is maintaining a constant chain of observation of the aircraft. Alternatively to relying on one constant observation, we can rely on multiple observations, if we can establish that these observations overlap - ensuring that there is no point at which the aircraft was not monitored in some way.
So now let's look at the flights.
Firstly, all four of the aircraft were tracked through the entire duration of their flights, from departure to crash site, via their respective airlines. Using this information, each of the airlines was able to confirm the fate of their aircraft, confirm the flight number, the location it crashed, and at what time.
In addition, partial radar tracking was maintained on all four flights.
Flight 11 and Flight 93 were maintained on radar from their departure until each flight dropped below effective radar coverage of the aircraft. Each aircraft dropped below radar coverage in the vicinity of their respective crash sites, within an acceptable time frame of the crash time.
Flight 175 was maintained on radar from departure until the moment that it impacted WTC2.
Flight 77 was maintained on radar from departure until the moment that the aircraft's transponder was deactivated. There then followed a period of nine minutes in which AA77 was not visible on radar. After this nine minute period AA77 was again tracked on radar until the moment of its impact with the Pentagon.
Visual observation was maintained on several flights for short periods of time. Additional observations may have occured which I am unaware of, however the following are established:
Flight 11:
Was observed by Flight 175 crew descending rapidly approximately 8 minutes before impacting WTC1.
Flight 175:
Was observed by Air Traffic Control Tower staff at Newark International Airport from shortly before impact until impact.
Flight 77:
Was observed by pilots of an Air National Guard C-130 transport aircraft from several minutes before impact until impact.
Please note that all of the above specifically relates to air traffic control observations of the aircraft, as per the question, and is not intended to represent an exhaustive list of all observations of the four flights, nor a complete list of all evidence linking each of the four flights to each crash site.
I believe that the above evidence establishes a solid "chain of custody" regarding the tracking of each flight by Air Traffic Control from prior to hijacking until impact.
As a final note I'd like to apologise for my use of the term "chain of custody". The phrase is not fully suited to this context, but best reflects the concept I wished to convey.