In the movie, Matrix Reloaded, they say that machines are drilling on top of Zion. In first part, Smith was trying to find location of Zion, he fails.
So how come machines have found location of Zion?
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The machines, especially the Architect program, already knew the location of Zion during the events of the movies.
The only reason Zion was allowed to exist because it served a purpose for Matrix. Zion was allowed to exist by the Machines as a giant pressure-release valve on the entire system, allowing the humans who realized the Matrix wasn't real (statistically, only a fraction of 1% of the whole human population) to be conveniently removed and isolated. It should be pointed out that the real threat to the Matrix is not Zion, but the systemic anomaly created by 1% of the population subconsciously rejecting the Matrix.
Once the One is found, trained and sent on the Path of the One to the Architect's chamber, Zion is scheduled for destruction (for a fresh start). When the One reaches the Source to disseminate the integral anomaly, he reinserts the Prime Program, which is the Architect's way of referring to the Path of the One. The Path of the One is a subprogram within the larger programming of the Matrix that ends with the One's arrival at the Source. After disseminating the integral anomaly at the Source, the One reinserts the Path of the One into the programming of the Matrix by choosing 23 individuals to rebuild Zion.
According to the Architect, Zion was completely destroyed 5 times before when Neo reached him. Unfortunately for the machines, Neo broke the cycle and Zion wasn't destroyed the 6th time.