I don't think so...when you fight the "dark characters", I think the doors just lead you to places that are close in proximity. They might reappear if you run-through the maze more than once (as in you go back to the SSE Map and return), I'm not sure, though.
Anyway, make sure you USE the map on the pause screen! I finished the SSE recently, and I just thought the map was "there" at first and that the Great Maze was "linear", that you had to actually remember how you got to where you were and where each door led you. Then I found out like a n00b that the pause screen maze map isn't just for show.
Just make sure that in the map, all but 1 of the doors (little circles) link to each other, and pay attention to a certain room's background. Hope that helps, and good luck!