I hope having a transporter device is more like folding space than particle-scanning and reconstruction. The scanning and reconstruction would still be great for replacing or repairing lost or deteriorating structures. Regardless, I have a number of questions that come up as we learn more about how our brain might work.
If our brain is changed in (near) death how would we determine what was lost?
Could we even reconstruct consciousness (this could be also gradual, but what is the speed of consciousness)?
It seems more like we would have to gradually move our conscious processing from per-existing wetware to whatever replaces it (even more wetware). It should behave like our brain as much as possible, but I don't think we could avoid being different from what we were.
Our own brain changes over time, do we think the way we did when we were 5? How different will we think far later in life (assuming our brain is at least healthy)? I think we would have to accept changes in our fundamental being (which is already very challenging). The difference is that not only could we live for longer physically, but within the pure consciousness an entire lifetime could be lived in less than a second. We experience this temporarily in dreams, or while experiencing a life threatening event such as an automobile accident or the final moments of death itself. What if that was extended over physical months, years, decades? How would we deal with such a inheritance, who would teach us how to cope and find meaning?
Would we want to live life at the speed of the physical world after such an experience?