In Summary:
Ruphas is the original, she got isekai'd to Japan as a Japanese man and grew up playing a game about her world, then "she" got isekai'd back to her original world after 200 years have past. "He" didn't "become" Ruphas, "He" is Ruphas originally
Edit: To add more context about this: the male Japanese man at the start of the story and the player of the Ruphas character is a very small part of her very powerful soul. The Ruphas of the world was pretty much aware of what the goddess planned for the world so she hatched up this kooky scheme about reincarnating herself as a man with none of her memories out of curiosity in order to roundabout foil whatever plan the goddess conceived by having herself be the farthest of what she is (human, male, from another world with no magic) so she can objectively look what she did wrong and how she can outsmart this pesky goddess who can seemingly rewrite reality according to her whims. So when the part of her that got isekai'd returned to her and throughout the story the protag seem to notice that he's slowly merging with Ruphas but in actuality, "He" is returning back to where "he" originally came from.