actually i've been wondering about this for a while, though on a different point of view.
what if your mind becomes the I/O of a computer? you wouldn't need a mouse, keyboard nor touchscreen to use a computer.
whats more is that every task would be so precise that you wouldn't need to zoom in and click that damn tiny pixel.
on another note, what about piloting a droid through the internet? you'd be sleeping in a capsule forever and use the droid similar to avatar, replaceable to boot, and skin customizable! damn gonna be a smexy machine.
now onto the technicalities:
if they could make the interface between the mind and machine small enough to fit a sunglasses and add in a function of injecting images directly into your mind, similar to having hallucinations, and make the interface a wireless tool then you get whats similar to Mnemosyne's 4th arc.
Basically, remotely working a computer (e.g. a server) using your brain. Aside from the interfacing we're not that far off.

Well, as I said in the Ghost Love, hmans ARE, for all intents and purposes mashines operated by complex computer, only difference beween this and conventional mashines is the organic building material.
Why would it be disturbing to move the programming from one mashine to another, if such a thing would be possible?
On the other note, if you were able to copy the mind completly with all of it's features as they were, while destroying the original, the copy would be the original, especially if the person in question believed that. Question is whether the term "copy" applies at the first place.
Oh, and yes, immortality is overrated. Most people don't really think about the consequences much. On the other hand, immortality, in a sense no-aging with a chance to end it all at will is a whole different matter.
Yes, the material science is mostly relevant to the manufacturing (i.e. not the architecture) than to functionality.
On the programming side of things, I figure the 'soft-drivers' are part of the brain's contents, otherwise the logic would be handled by the hardware architecture; nothing would be really left behind.
I believe a minimal necessity to distinguish the original is related to causality, otherwise, if there were absolutely nothing tracing back to the original's designation, it might as well be impossible (or just plain annoying) to figure out.
I think that is what would happen if a human mind came into a computer;
After a while, you would get really bored, and the only thing you could do to have fun,
is to make pranks on the people who owns the computer.
In our typical personal computers, the CPU essentially does this: read memory, do something, some kind of caching => repeat; that's pretty boring already with that regard. But don't think we're focusing on
personal computers, or appliances for that matter.
Some people have this impression that there will be some moral or cognitive dissonance with the innovation of some of the more science fictional technologies. I recall the beginning of Asimov's I, Robot anthology, with a white-bread suburban family getting their ontological hackles raised by the new Robo-nanny and labour unions being labour unions - the technology was banned on Earth until decades later where they're the benevolent rulers. We read Frankenstein complex stuff, which began with the eponymous novel and will remain in popular fiction until Judgement Day. Fear of objects becoming subjects, of breaking through the illusion of the soul as a metaphysical property stuck in unwholesome and squishy flesh assembled haphazardly in some woman's uterus. The usual result is something like Khaaaaaaannnnnnnnnn nnnnnnnnnnnnnnnnnnn nnnnnnnn!, the Borg, T-1000's, or Mitt Romney. We assert that humanity is something special, and like every Shakespeare play, throwing the natural order out of commission can only lead to bad things.
The problem with that perspective is it ignores the observed evidence. We've been living in a science-fictional age for a generation or two now, with innovations happening faster than epochs of human history. You know what? We're adapting like a boss. There are concerns sure, but for the most part people are clambering for the next gadget with the new doodad attached. I believe this is an instinctual, primordial, lizard-brained response to our most basic evolutionary advantage. We use tools, we love tools, we're not sabre-tooth chump meat because we gots sharpened sticks and knew damn well which edge was the pointy one, we didn't freeze to death 'cause we received our merit badge in fire-craft. Every time technology gets made, and we see someone else use it to improve their condition, we want to replicate them.
Downloading your consciousness into digital form? It sounds strange, but so would an internet forum on a anime-based torrent site be to someone 40 years ago. That's because he or she haven't gone through the chain of steps required for such a thing to exists, not just technologically, but culturally. Assuming bio-digital trans-mutation is possible, by the time we get there these kinds of discussions will be mere trite academic arguments for philosophy students, the culture will have moved on. People who see the advantages in being raptured digitally will be selling their unneeded organs to get in the queue.
The same goes for bio-engineering, if we choose to go that route. Hell, otaku will be getting their children with candy coloured hair and unnaturally bright, large, and colourful eyes.
Considering the way technological advancements are supposed to trend, it actually would be quite dismal if there were no beneficial breakthroughs in all the related areas as well (the possible abuses are another story). Nevertheless, unless we are discussing about warfare devices (hell, even computers were being in development since WWII), overall there shouldn't be anything in innovations that would be worrisome. So yes, moving toward something which might appear science-fictional should not inherently be bad, and being disturbed by it is simply silly-- nonsensical, baseless, or recalling media if preemptively so.
IMO the "soul" as we know is likely just the shit that is damaged in the entire body. In short every little imperfection is what defines an individual on a cellular level. Which is what we perceive as the soul. Again that is just IMO.
As far as I am aware, there is no universal definition of 'soul', and philosophers seemingly go nowhere concerning this as they also try to also accommodate some religious perspectives. Of course, this is merely my observation.
Anyway, should I use the word 'soul' anywhere, I would just be using it as a combination word for [all possible states of] mentality + personality, among other things which would be characteristic to a sentient entity.