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Perhaps Morpheus was incorrect, and that 100 years was the last cycle. Perhaps he was unaware of the cycles, is what I'm saying, infact I would bet on it, as it seemed the architect was revealing it to Neo at a moment when it could no longer help Zion.
Yes. Morpheus was indeed totally unaware of the cycles and the true role of The One. as far as Morpheus was concerned he thought Zion was created by The One who presumably broke out of the Matrix somehow, freed a bunch of humans in the process, and starting a new city deep underground away from the machines. Morpheus thought that according to the prophecy another One would return and this time help end the war with the machines.
But as you point out, Morpheus had no idea there were... previous Zions. Or that upon the return of The One Zion was destined to be wiped out and restarted from scratch.
Somewhat ironic then that no sooner had Morpheus discovered the prophecy was a lie, when it actually came true. Just not in the way he ever expected it to.
So its still plausible that Morpheus is incorrect about how long his Zion has existed, but personally I doubt it, and assume that 100 years is just a rough figure anyway, and generally accurate.
~we are a part of the process, not instigators of its progress~