When I first saw machines dig a four-kilometer tunnel down to Zion, I couldn't help wondering if previous Zions were taken out the same way, and if so, how could Zion citizens not notice such tunnels and previous Zion locations? If Zion had been rebuilt several times as the Architect says, it seemed to me that it would be extremely difficult for the machines to prevent current Zionists from discovering clues about five previous Zions, whether it be tunnels, graffiti, wreckage, or someone's old diary device, not to mention the gigantic cavities in Earth's mantle that made up past Zions.
However, remember that the first 23 humans freed from each Matrix always believe that they are the first to be freed. We also know this selection process occurs very shortly after the previous Zion was destroyed, so there would probably be 250,000 dead human bodies for the first 23 humans to discover and joyfully clean up. This wreckage and human death would make it look very believable to current Zionists that humans built an underground location as their last refuge of resistance against the machines after the skies were scorched.
Even under this theory, machines would still have to re-fill and pack the dug tunnels with dirt and rock so that digging could still be used as a surprise tactic to destroy the next Zion. As far as the old Zion mainframe and other computers are concerned, the machines wouldn't necessarily have to erase all data pertaining to knowledge of the Matrix, because the last phase of human resistance could have discovered the fields of human pods and could have even learned how to hack the Matrix.
Remember, initially, it was hard enough for you and me (the omniscient audience watching the movies) to swallow the idea that the One and Zion are all part of one continuous cycle that the machines control. It would be even harder for the first 23 freedom fighters to believe that all the wreckage and human bodies are merely the end of a 100-year cycle that they are about to start all over again.
SAQ: Zion's Atmosphere | SAQ: Zion's Population |