More importantly, does anyone suggest that running the original brain and the copy doesn't result in two separate diverged intellects? If running two results in separate consciousnesses then obviously they are not the same.
I don't think that follows. If "your" consciousness is just the consciousness that has a continuity of memory with a previous version of you, then the two copies would both be you, but they would not be one another.
Let's say that I a suitably advanced fMRI is developed that is able to map out the connectome non-destructively, I use this device on you to create a copy of your mental state, and then let you go about your day. At some point later I turn on a whole-brain simulation from this data. What do you, the you-that-walked-into-the-scanner expect to experience?
I agree. But the further implication is that for the same reasons, if your brain is plasticised and later scanned and turned into an uploaded whole-brain emulation, you'd still be dead. Uploading is not a pathway to personal longevity, or whatever you want to call continuation-of-me-not-just-my-memories.
That's the crux of it all, isn't it? Is your self any more than your personality and memories? If so, then you'll have to resort to a soul or some such. If not, then the upload is really 'you', or a copy anyway.
And who's to say a soul wouldn't attach to a copy anyway? Souls are not that well understood. Perhaps it would be fooled by the copy, or have an affinity for it, or some such. As long as we're speculating.
No, there are plenty of perfectly reasonable physical theories for the nature of consciousness that don't equate identity with memories and don't involve souls. There's no reason to resort to dualism.
For example, there is the identity-is-the-instance-of-computation theory which says that it is not the information being computed (memories) that is relevant, but the computation itself.
That's obvious to me, but I've learned that it's not obvious to everybody. It's an instance of the mind projection fallacy that your or I think that is a simple obvious truth but others think the opposite is just as intuitive. I sometimes wonder if different people have different experiences of consciousness and self-identity...