1. Morpheus has found other people he believes to be "the One" before. He was wrong, and they died or otherwise didn't pan out. (I'm fairly sure this is still referenced in the movie? Just not the specific deleted scenes that the article mentions.)
2. There is a larger cycle of "the One" resetting Zion as part of the machines' system of control. This has happened a bunch of times now.
These are different things. They have nothing to do with each other. They are neither mutually exclusive nor mutually supporting.