A windowless cockpit as such is probably not inovative enough to deserve a patent.
I recall reading, several years ago, about an experimental B737 that had the flight deck duplicated somewhere back in the fuselage. The "classic" flight deck was retained, for safety reasons, but it as demonstrated that the aircraft could be successfully flown from the experimental flight deck in all phases of flight.
Also, an early concept for Concord(e), even before they agreed on the final "e", was that there should be no windows in the droop nose. The flight crew would have sight of the outside world only in subsonic configuration.
So, unless there is a lot more to it, the patent claim should fail on the grouns of "prior art".