First, Neo never did die. The brain lives on while the heart stops. We see this all the time in movies and medical shows that always show shock
treatment being given to people whos hearts have stopped. Neo simply wasn't "pronounced" dead yet, medically speaking. Who knows exactly how conscious
a person is when their heart is stopped.
In The Matrix Online (a video game that takes place after M3, with a storyline that has the Wachowski Brothers' approval), the machines give all redpills emergency jack-out protection - in other words, just before they die (no matter how the death occurs), they wake up as their RSI is automatically transferred back to the real world. If this can be done for all redpills who jack into the Matrix ver. 7, it seems unreasonable not to assume that the One isn't given this same protective measure in ver. 6 and all previous versions.
Furthermore, dying is a bendable/breakable rule in the Matrix just like every other rule. While most other redpills hacking into the Matrix cannot overcome the rule of dying, some probably can, and as Neo gained power from the rejection code that was funneled into his consciousness, part of that code may have included the anomalous ability to overcome the illusion of death. Neo's rejection of the Matrix could be so strong that he can reject even death itself. I think this is what enables Neo to block Smith's attempt to copy over him.
In M2 after Trinity dies, Neo starts talking to her and says, "I know you can hear me." How exactly does he know? It seems that he is referencing the time when Trinity spoke to him while he was dead, suggesting that Neo could hear Trinity speak when he was in that state. What this implies is that Neo's "half-dead consciousness" was taking place in the real world. Once Neo realized he didn't have to die, his RSI was reinstated inside the Matrix.
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