That was pretty much my theory. I don't think we've ever seen anyone originally from CHS go through the portal, so for all we know, it changes humans into Earth ponies or some other minor tweaks to their appearance. Given her personality, she might be suspicious of the mysterious talking ponies and give herself a different name. As Celestia knew the Equestrian's Sunset, she could have guessed that she would never change her identity. The human Sunset might have escaped the castle but went back for whatever reason, and then Celly wasn't in or something, so Luna, who didn't fully recognise her, wrote it off as amnesia.