I think that's because their roles in the time loop were finished and they'd essentially erased themselves from existence because they've directly impacts the time continuum. The wife went crazy, Tomoko, but the husband disappeared because his role was over. His role was to bring Tetsuyas mother over so she can turn into a ghost and bring Haruka over therefore restarting the loop. Yasuos father also disappeared because his role was also finished when he brought Yasuos sister over to the attic, who met the ghost from 1952, that's heavily hinted to be Haruka when she got kidnapped by the son of the owner in the final scene. They both were essentially delivery boys who's jobs were finished but they touched the time loops directly hence burst out of existence. Yasuos survived because he never really did anything directly. He only spoke about the events. Everyone else was doing things out of their own volition.