Cypher isn't a former One, he was the one who could have been the One, but the other one's didn't believe he was the One, they thought it was someone else. DAMMIT.
Cypher did not die. He became a black cat inside the Matrix. That is why the Matrix rebooted at the end of Revolutions. Because the Black Cat, being the residual imagery of his digital self, was Cypher, a former ONE, capable of injecting the code into the Mainframe.
All that rot with Neo and Smith and Dues Ex Machina was just side story of no significance.