To futher clarify....
If you hear a 96xx flight number, it is a stub- that flight to the gate and the passengers is it's original number (e.g. 831 or something). For ATC purposes due to the inbound portion of that flight being delayed, they will use the 96xx number on freq.
A 98xx flight number is a chartered flight- typically carrying sports teams.
A 99xx flight number is a repo flight. You'll typically see a charter flight going into an airport with the 9800 number and repoing back out with a 9900 number b/c it is now an empty repo aircraft.
Nerd time, off.