That's why his argument is described as controversial. He argues that known laws of physics are inadequate to explain the phenomenon of human consciousness. Neuroscientists would, of course, disagree. The changes in neuron shape that accompany new memories are significant and obvious.
By the way, the "new" substrate could just as easily be organic if that turns out to be the easiest approach. But the atoms from which it is constructed need not be the original atoms. Most people would more readily accept the argument that this new organic brain was the same person as the old one.