If EMPs cause long-range damage to all electrics, move them further away from Zion so that they don't destroy the command centre, holographics et al. It's perfectly simple. Of course they did send the hovercraft with EMPs to shut down the machines, but Smith/Bain screwed that up. But still, in a city that's standing against an army of beasties which can most easily be shut down with EMPs, then surely it makes sense to fit EMPs so they get the enemy before they reach the city. It's simple, surely.
Okay, now I do have a question - if an explosive device takes out part or all of the human-pod places (not the fields), what happens to the "humans" in the Matrix world? They can't just appear to die, because without feed from their brains, their "program" can't exist in the Matrix. Do they, like the glorious Lord Lucan or the lovely ladies of Hanging Rock, just disappear?
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