I hope that I am mistaken and that there is more to the movie than my speculation.
I think that the original characters are still dead.
The Matrix is a pool of information and memory is the retention of information over time.
In this new movie, the current characters are programs: backup copies of the memories of the characters that we saw in the previous trilogy.
It would explain why Morpheus looks so young (and is played by a different actor).
In the original trilogy, it was already revealed that Mankind & the Machine World are not as different as they think they are and, also, that it is possible to download an artificial consciousness to a biological body. So, it is obvious that it is also possible to keep a backup copy of the memory of a human being.
At the same time, it can't be the only twist, can it?
I suspect we will find all incarnations of the characters are computer generated. Maybe the real versions will turn up in this movie. That is based solely on a few comment's made in the second and third movies.
I also do not believe that was intended in the first movie.