Persona 3 Reload has replaced a genderqueer character, possibly in order to avoid offending new players coming to the remake of the game.
In the original 2006 game, there’s a beach scene where Junpei Iori, Akihiko Sanada, and the male protag strike out after trying to flirt at the beach. Luckily the trio come across a woman who seems amicable to fooling around with the boys. However Akihiko takes note that she has stubble and deduces that she’s trans (it’s unclear whether they’re trans or a crossdresser). Either way, the boys aren’t interested any more and they run off.
The scene has been criticized for transphobic stereotypes, especially since the character isn’t forthcoming and when identified they persist and try to convince the boys to try something “spicy” with them. You can see the Persona 3 Portable version of the scene below.
Rather than recreate the scene or trying to update the original premise for modern audiences, Atlus sidestepped the issue entirely by changing the character’s entire identity. Rather than a flirty beach babe, she’s now a strange conspiracy theorist, eager to let the boys rub sunscreen on her body; but not without first explaining how the sun is actually a government conspiracy and it was replaced in the 1980s.
After she goes full mask off with her conspiracies, the boys are understandably no longer interested and run off. The scene creates the same result as the original, but without any commentary (no matter how offensive) about the character’s gender.