However why on earth would brain uploading be done all at once. Given the right nanotech you could begin at one part of the brain - slowly replacing biological neurons with artificial ones.
Once all your neurons are artificial - just download their state. This is pure speculation and way out in the future - like 100 years - but it could be fun :-)
You know what is a really awesome piece of nanotechnology? All the proteins and enzymes that are making your neurons function, right this very moment. How do you download their state? Look at their conformation and who they are interacting with.
Nanotech isn't just making a computer smaller. Much of your body already operates on the "nano" level, and does it pretty efficiently.
I'll admit nanotech really isn't my field, but I understand enough of it to know that it isn't a panacea. If a materials science person wants to jump in on this I'd be appreciative (to either confirm/deny what I said)
My main point was that brain uploading need not be done all at once.