I don't think this is what's happening here but I did once see something else where at the start, it did seem that the main character was magically turned into a girl and apart from his best friend who was there at the time, everyone else's memories and all the physical evidence made it look like he'd always been a girl; only he and his best friend knew the truth.

Turns out in the end she'd always been a girl and the magic had been to make her and her best friend think she'd really been a boy until their memories and their physical reality had been altered. Well, it would definitely be a lot easier to alter the memories of two people than to have to alter the memories of every single person who'd met the main character and all the physical evidence, that's for sure.