Thanks for the response, I was starting to worry I'd scared everyone off! 
I think the disguise should work in this circumstance, as the story is of high fantasy genre with elements of piracy on the high-seas. People will have to suspend their disbelief for characters throwing magic around like candy, so hopefully can bring themselves to believe that a young (late teen) woman can successfully pull off pretending to be a man of similar age.
It's hard to describe everything that's going on without writing out a novel right here, but basically the young woman has a twin brother. He is heir to a contested throne and she is used a decoy due to an uncanny resemblance between them, aside from the obvious differences. The (unnatural) uncanny resemblance is a key plot point in itself, which will be revealed later in the story.
In order to aid this deception, insisted upon by the King and his latest wife to protect the only son and heir, the young woman?s death is faked to the nation while she was a child. She was then kept hidden and trained in secret to mimic her twin from an early age.
Shortly before the start of the story, she was shipwrecked while out pretending to be her brother at a naval battle. She was later picked up by an uninvolved nation and ended up giving her name as a young knight from the palace she has feelings for, while continuing to appear to masquerade as her brother to throw off anyone hunting him.
A bunch of stuff happens while she?s trying to get home, including her discovery that home is not safe and her brother is missing. She gets various travelling companions on the way. Then her love interest dramatically arrives on the scene and announces his name, prompting her to admit to everyone that she?s not the person she was claiming to be.
She then tells everyone she is her brother! Her love interest knows her and her twin well enough to realise this is a lie, but just frowns and stays quiet.
It?s up to that point that I?d rather keep her gender a secret. After that point I?m intending a reunion scene with her and her love interest in private where the truth will come out, so the reader will know the basics of what is happening ahead of the other characters.
I?m currently leaning towards keeping her in the background until that point, not writing from her point of view but showing her from the other characters points of view. That way, I should be ok to refer to her as a He?
After the truth comes out, when writing from the young woman or her love interest's point of view I can presumably refer to her as a She. But what about when I'm writing from the point of view of a different member of the group, who assume she's actually a he? Do I still refer to her true name and write her as She outside of their speech?
It gets confusing again later on when her brother turns up and they keep switching places. Presumably it's best to keep the writer in the know at what's going on?
Sorry that was so long!