For all I know, there is some NCAA "hidden policy" (like the mysterious "Graduate Transfer Rule," although I think that's just, "Anybody who has just received their Bachelor's Degree can claim anything as a field of study that their current school doesn't offer - I like to say that, since it has to be something not at their current school, they are switching to a branch of minerology called Ring Studies) that says that they do go by what the teams' records are on the second Sunday after Thanksgiving.
However, if there isn't, and Navy would have won, I think Navy would have realized that its two choices would be (a) decline the bowl bid, or (b) have to explain to all of the Minnesota fans that have bought tickets and made plane and hotel reservations that they now have tickets for a game between Bowling Green and Navy. There is a third option - get the NCAA to create a 42nd game, the way it did in 2021, and invite the next team on the APR list (South Carolina, IIRC) - but that would be highly unlikely.
The NCAA can stop worrying about this for now and go onto more pressing football matters - mainly, figuring out what the new bylaws that would allow teams to participate in the full length of the CFP playoff would be.