I think it means that yoru might have been unborned by ikuto while searching for his father.cause amu and tadase were searhing for ran,miki,and suu in a place were all unborned charas which were seen in the past chapters. I think while amu and tadase were spared that yoru might have been with amu at the moment. While amu was with tadase's older self she said that something touched her. I think yoru was trying to kept up with amu. This is what I think happned in chapter 46