Possible alternative
Not sure if this is possible (only fly domestically) if this was well planned, couldn't the pilot/hijacker have already entered a flight plan into the system earlier that day, then when at the cross over from one FIA to another, turn off the xpndr, change course and altitude, then fly along for a bit (with all other communication turned off) then at another FIA boundary call along the lines of "xxx centre, this is embraer 107 at FL290 for xxx, we are experiencing xpndr issues..." The controller looks up the flight plan and pilot flies along giving position reports etc under the previously entered flight plan call sign? Would the new controller check with the previous region? The best way to hide a tree is in a forest, they simply became another flight with a malfunctioning xpndr (unless they can mod the hex code or just run mode c) and proceed normally. What other flight plans or flights just happened to be going the same direction on the same day and time?
As good a theory as any or completely off the mark?