Suppose you had an identical twin with identical genes and, until very recently, an identical history. From the perspective of anyone else, you're similar enough to be interchangeable with each other. But from your perspective, the twin would be a different person.
The brain is you, full stop. It isn't running a computer program; its hardware and software are inseparable and developed together over the course of your life. In other words, the hardware/software distinction doesn't apply to brains.
To call something an "uploaded brain" is to make two claims. First, that it is a (stable) mind. Second, that it is in some important sense equivalent to a particular meat brain (e.g., that its output is the same as the meat brain, or that its experiences are the same as the meat brain's). The sorts of methods you're talking about to stabilize the mind help with the first claim, but not with the second.
I've always struggled to make sense of the idea of brain uploading because it seems to rely on some sort of dualism. As a materialist, it seems obvious to me that a brain is a brain, a program that replicates the brain's output is a program (and will perform its task more or less well but probably not perfectly), and the two are not the same.
What if there would never be someone I trusted who could tell me I was Good Enough, that things were in some sense Okay?
The internalized feeling that you're not okay is a huge part of what motivates you to become better. If you lost it, you would be much more likely to become complacent and stagnate. Both inner peace and relentless drive are profoundly valuable, but they are mutually exclusive.
I certainly agree that brains are complicated.
I think part of the difference is that I'm considering the uploading process; it seems to me that you're skipping past it, which amounts to assuming it works perfectly.
Consider the upload of Bob the volunteer. The idea that software = Bob is based on the idea that Bob's connectome of roughly 100 trillion synapses is accurately captured by the upload process. It seems fairly obvious to me that this process will not capture every single synapse with no errors (at least in early versions). It will miss a percentage and probably also invent some that meat-Bob doesn't have.
This raises the question of how good a copy is good enough. If brains are chaotic, and I would expect them to be, even small error rates would have large consequences for the output of the simulation. In short, I would expect that for semi-realistic upload accuracy (whatever that means in this context), simulated Bob wouldn't think or behave much like actual Bob.
Surely both (1) and (2) are true, each to a certain extent.
Are the random thermal fluctuations pushing me around somehow better than the equally random measurement errors pushing my soft-copy around?
It depends. We know from experience how meat brains change over time. We have no idea how software brains change over time; it surely depends on the details of the technology used. The changes might be comparable, but they might be bizarre. The longer you run the program, the more extreme the changes are likely to be.
I can't rule it out either. Nor can I rule it in. It's conceivable, but there are enough issues that I'm highly skeptical.
Let's try again. Chaotic systems usually don't do exactly what you want them to, and they almost never do the right thing 1000 times in a row. If you model a system using ordinary modeling techniques, chaos theory can tell you whether the system is going to be finicky and unreliable (in a specific way). This saves you the trouble of actually building a system that won't work reliably. Basically, it marks off certain areas of solution space as not viable.
Also, there's Lavarand. It turns out that lava lamps are chaotic.
That wasn't well phrased. Oops.
Any physical system has a finite amount of mass and energy that limit its possible behaviors. If you take the log of (one variable of) the system, its full range of behaviors will use fewer numbers, but that's all that will happen. For example, the wind is usually between 0.001 m/s (quite still) and 100 m/s (unprecedented hurricane). If you take the base-10 log, it's usually between -3 and 2. A change of 2 can mean a change from .001 to .1 m/s (quite still to barely noticeable breeze) or a change from 1 m/s to 100 m/s (modest breeze to everything's gone). For lots of common phenomena, log scales are too imprecise to be useful.
Chaotic systems can't be predicted in detail, but physics and common sense still apply. Chaotic weather is just ordinary weather.
That's the point. Nobody thought such tiny variations would matter. The fact that they can matter, a lot, was the discovery that led to chaos theory.
The ancients considered everything to be the work of spirits. The medievals considered the cosmos to be a kingdom. Early moderns likened the universe to a machine. Every age has its dominant metaphors. All of them are oversimplifications of a more complex truth.