At the end of Revolutions, there's no need for The One's code to be reinserted into the Matrix.
The machines have agreed to end the war and dismantle the Matrix as well as actively working to free those humans who remain inside it. The problem of the "unbalanced equation" (e.g. that Neo was supposed to fix) has resolved itself, albeit in a very unexpected way.
It's clear that some people will struggle with the shock and will even actively resist being removed. As we can see from the (wholly canon) Matrix Online, after the events of 'Revolution' the machines and Zionians started by actively freeing the 1% that are already subconsciously aware of the Matrix and moved on from there.
The ultimate result of the failure to resolve the "systemic anomaly" in MXO (Matrix Online) was that eventually every single person left plugged into the matrix had godlike powers to influence their surroundings, at which point everyone has become aware of the unreality of their situation and is (at least in theory) able to be unplugged safely.
If you're interested in "what happened next", you can read the plotline of the Matrix Online game here.