Well, isn't that the whole idea? Objectively, there is no difference. If there was, uploading wouldn't ever be possible.
The only potential difference is the subjective impression of "this consciousness that I am now is the same consciousness that I was yesterday" versus "this new consciousness is an exact clone of mine, but is not really 'me'".
This incremental upload technique simply tricks your subjective self into thinking there is absolutely no change in continuity.
In other words, your subjective consciousness is somehow changed but you can't subjectively tell? What does that even mean?
If one of your neurons randomly dies right this instant, you would probably not subjectively notice, even though that neuron composes your subjective consciousness. Your neural network is highly redundant and fault-tolerant.
It depends where those neurons were sent off to in the meantime and what they were doing, but with such a big jolt, it's quite possible they would perceive themselves as "clone" (after understanding the situation at large) while you in your new machine self would be the "original you".