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What happens when the matrix is Reloaded? Is there going to be some big changes in the Matrix? Or does everything just continues living like nothing happened.

but what would happen to the people inthe Matrix, will they just lose their memories???

Why not? As long as the pod-humans live happily in oblivion they produce energy. Only some programs seem to keep their memories (Smith, Merovingian).

But if they lose their memories, than everyone would be an amnesiac. no one would remember anything about their lives, family or friends. No one would remeber how to do anything.

Well, they may just wake up with new pre-programmed families, skill and knowledges, as they have for the past five runs on the Matrix.