This can be a pain.... Over the holidays WN decided to take flight 786 from BUF to PDX and remove it from the scheduled flights. This has a stop in Midway and you could book BUF to MDW or MDW to PDX, but not the entire flight together.
Not sure why, maybe revenue management optimizing things.
It took me 3 calls to finally get on the line with a very curt agent who I would not let off the phone. I kept asking how they could have the same flight number for two different flights on the same day if it wasn't meant to allow the entire travel. Finally they gave in and manually did it. But it showed up on my itinerary as two flights both with the same number.
Then on the flight when they did the headcount on through passengers on the plane they said there were too many and asked the people name by name who everyone was. When they got to us (my wife and two young daughters) they told us we were incorrect, should not be on the plane and to get off. When I said we should and it was booked with a WN agent she then asked for my boarding pass to prove it. Well, I nicely replied that I gave them to the person at BUF checkin while boarding the plane (??? - what were they thinking). That was met with get off the plane and take it up with customer service. I asked if my wife and kids could stay while I got off, which I am thankful she said yes to, and went to the gate agent who confirmed we were on the plane but somehow it was booked as separate segments instead of through passengers. I got back on and all ended well. But it was a hectic day given there were such long lines that even 2hrs early at BUF and we almost didn't make the plane and we almost got kicked off and forced to board last losing our seats together (I didn't get back on until after C boarding due to the amount of time it took to resolve it with the gate agents).
Enough of my story/rant - in short, it can be a real pain when asking for unscheduled routing for awards. Its nice to see that there is a T&C allowing it because none of the 3 agents I spoke with when booking the flights knew this.