[Captain Walker]

Maybe they had a couple of "hangar queens" on board that couldn't make the flight with the squadron (although the F-35 is just too new for that).

I don't know; it sounds like they had something on board that was expensive.

[Spktyr]

The ship was undergoing refit to be able to fly the F-35B. None of the aircraft was aboard and the flight deck was covered with equipment, gear and supplies being used in the deck conversion.