The flight plans should be on the plane's own internal computer, which should be receiving encrypted data from American Airlines' own servers this would, among other things, prevent the update issue you mentioned. The Cloud is all well and good if you're sending people weather reports or news but Civilian Airlines should have the same sort of fully internal systems as the military does, you shouldn't be using a third party like Apple to actually run the system.
You'd be surprised just how much third-party software and hardware the militaries of the world use.