The outbreak among trainees comes two months after Defense Secretary Pete Hegseth made the annual flu shot optional for U.S. military personnel.
The service announced the delivery of the Qatari-donated aircraft to Joint Base Andrews on Friday and the kickoff of its commissioning flights.
The remains will be airlifted to Dover Air Force Base for further identification confirmation and preparation for return to their families.
The individuals who died in Monday's B-52 Stratofortress crash were a mix of service members, government civilians and contractors.
