The fact that there were five predecessors in the shooting script, and five predecessors in Reloaded / Revolutions, very strongly suggests that they lifted and reworked that plot from the first movie, for reuse in the sequels.

From a narrative point of view, it would be confusing as hell to have five predecessors in this iteration of the matrix, as well as five predecessors across five previous iterations of the matrix.

Could both have been part of the same overarching, pre-planned plot? Sure. But is that likely? Not at all.