The code they were referring to was the name used by the Secret Service to discuss the location and itinerary of Air Force One on a given day. They do not simply call it Air Force One. For example when Clinton was in office they probably used quaint indentifiers such as [i]The Draft Dodger[/i]. Now they probably call it something like [i]The Ass Whoppin' Texan.[/i]
On 09/11/01 they received a call from someone stating that Air Force One was a target. In order to confirm it was a legitimate threat they asked the called if he knew the code and he did. It has nothing to do with any type of "Codes" on the plane, simply the word(s) being used that day to identify it with internal people.
As a side note when Air Force One was in the air during the Nixon adminstration they always called it [i]Dick Over America.[/i]