I think when all this things are over, he'll definitely miss his memory being Conan.
I have written a DC horror fan-fiction about this topic. Many years have past since the BO was destroyed. Shinichi returned to his own-self. He eventually married Ran and had kids. He is enjoying his fame (for defeating the organization), his fortune, and the happiness he has with his family. Everything go smoothly, until one day, when he sees Conan's ghost standing in his dark bedroom, staring straightly at him. (Conan's face is covered in blood). Since then, the hallucinations just keep coming and coming (which is described in detail in my fan-fiction)...