Presumably a retreat point is set during the scene where the lighthouse is lit on the world map, and retreating after the fight will put you back into the boss fight.
Possible solutions:
Change the Retreat patch to be more selective about when it sets a retreat point
Change the aerie event to force the retreat point back where it normally is (and also do this for any similar issues, e.g. the Apojii cave)
Presumably a retreat point is set during the scene where the lighthouse is lit on the world map, and retreating after the fight will put you back into the boss fight.
Possible solutions: