Didn't realise the manual mentioned this case in particular.
From memory, Haneda actually remains the slightly bigger airport, at least if you go by the order you get in the in-game airport lists. It changes to domestic, rather than becoming a smaller, secondary airport, the way somewhere like Milan or Orly does.
There'll be some frantic restructuring with either choice. Either lots of LH demand vanishes, or big domestic routes are cut to a fraction of what they were. Should keep life interesting, at least.