In the first film, Morpheus states that if someone dies in the Matrix, he dies in the real world because the body cannot live without his mind. How about the opposite? If the mind is plugged into the Matrix, it is equivalent to the program that runs in the world. (as evidenced by how Neo imagines others in the Matrix). If your body is no longer alive, it’s possible that the program is still running and hasn’t been stopped. One can argue that such thoughts / programs are people who are scheduled for termination but are assisted by entities such as Merovingian to continue to live their lives in a world of trust.
Back to the question, in the real world, Mr. Anderson / Neo has died since his body died from an injury. Is Neo still living in the Matrix? Unfortunately, when Agent Smith hit him into Neo, he basically removed the Neo “program” and deleted it himself.
We saw Oracle, Sati was restored when the Matrix was reset. Will Neo be raised too? Based on what the Architect said, Neo represents an anomaly made in the Matrix programming. Anomalies are integrated with the Source Code and there is a re-loading of the Matrix. In the film, we are at the point where the anomaly has returned to the Source Code, but does not reload the matrix. This will take us to the point where the One must be found again so that the cycle continues. Because Neo is no longer connected to “agriculture”, One must be someone else.