Good point about the sex- change thing. So...would you say, "I never knew that you are a girl?"
Yes, that's the logical, the semantically correct, thing to say. Actually, in most contexts I would probably say 'I didn't know that you are a girl.'
For example, you have an online 'friend' that for some reason you thought was male. Later you learned that she is female.
Sorry, for the late response; initially I apparently didn't read your post carefully enough to realize that you asked me a question.