Responses
I think he isnt exactly disappeared. If you read closely during the 3 months timeskip, Taichi said to let Yuuya out when Naoya is being nervous. This could imply that he is still within him. Although .. probably not as dominant as he used to be. (￣∇￣")
That way, its a happy ending for 3 of them.
I didn't like the end so much cuz I thought it's going to be like (Yamase wa doko e Itta?) where the two personalities will merge but WHYYY YUUYA disappeared (┬┬﹏┬┬), I know he is evil however I want him to have a good ending with them