Earlier quoted context omitted.
I'm certain each flight has its own completely unique ID buried somewhere in a database. But, shorter codes can be spoken into a radio faster and with lower probability of misinterpretation - both critical features for air traffic control. Those shorter codes will necessarily be reused, it's just a question of the time interval between re-uses of any particular code. I faintly recall seeing two Southwest flights from…
Short flights out-and-back from a hub can have the same number on the two legs. An example is AA 1992, which today departs PHL 3:06 PM, arrives ATL 5:17 PM, departs ATL 5:57 PM, arrives back at PHL 8:05 PM. (All times US Eastern.) My mother recently had an itinerary where both her flights were this flight - the PHL-ATL leg on a Sunday and the ATL-PHL leg on the following Saturday. (It looks like as of Tuesday AA 1992…
Unless the PHL-ATL flight is more than 40 minutes late, I don't think you'd necessarily have two planes moving through air traffic control with the same code at the same time. While the PHL-ATL flight lands and goes to its terminal, the ATL-PHL plane can be boarded, cargo can be loaded, and such. If PHL-ATL is less than 40 minutes late, you wouldn't even cause a delay for the ATL-PHL flight.