Of course, we are making the assumption an exact copy would be necessary. Large parts of the brain at any one time may be dormant, and other parts totally redundant. In many cases, the same processes may not need to repeat exactly to yield the same result. And of course, the vast bulk of the brain's operations may be involved in perfectly routine functions, like regulating metabolic activity. Neither do we know if brain function is resolved down to the molecular level. To use a crude example, a single component in an integrated circuit may be composed of millions of atoms, yet be reduced to a simple binary on-off state.

It's pretty fair to assume the phenomenon of consciousness, even if it is totally materialistic, may be so complex that it it cannot be duplicated. But neither can we guarantee that it is necessary to duplicate it exactly to make a copy which is indistinguishable from the original.

If two objects or processes cannot be told apart, they are for all practical purposes identical. If we are talking about two souls, we are left with the embarrassing conclusion that even the copied soul has no way of determining if it is different from the original.

My instincts tell me that when you start running into paradoxes and contradictions like this, then you are obviously missing something. It would be tempting to rely at this point on some religious or spiritual explanation. But it isn't necessary to explain the complexity or magnificence of the concept of consciousness. The natural, mechanistic explanation itself, that it is due to molecular interactions evolved over billions of years, has an elegance and beauty to it that makes the supernatural alternative seem almost childish, even trivial in comparison. If you need a god in your theology, it is difficult to think of one more complete and more sublime than the one revealed by chemistry and physics.