I think I've read same thing before, but can't remember it. However after skim through my list, I only can come up with similar plot:
.. I think she falls in love with the boy she thought was her brother.
Kimi ga uso o tsuita
I also come accross this title while searching: Junai Labyrinth, the girl loves her brother, however it has 'false incest' tag, so maybe it's the manga you looking for?