I think its a manga I read a while ago where the parents trick their daughter into believing shes a boy. So she ends up growing up as one.

I remember in it they rewrite a sex ed/book about puberty to answer questions she has about her body etc.

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Maybe this?

The Day of Revolution

I doubt it, since the parents also believed she was a boy, and there wasn't anything about a sex ed book.

Sort of but not quite: Rose of Versailles and Princess Knight. Girls raised as boys, but they aren't lied to about being girls in the end.

it might've been the other way around, a son tricked into believing he was a girl.

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Feed your head.

Maybe it's Hen. At one point of the story it's said that the father of the protagonist made her believe she was a boy for quite some time when she was a child.

yeah I think it might have been Hen. Now that I think about it, she did come up with a ridiculous story like that..

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Feed your head.