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You are assuming present day lasers. An advanced civilization will individually control the photons.

You also don't really need atom resolution anyway. You can build mechanical computers driven by rolling stones by abblating matter with powerful beams - lithography on continent size scale, etc.

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Even if you individually control the photons, I'm not sure that's possible. Matter still behaves like a wave at quantum levels. I don't know enough to say with certainty. This is all highly speculative.

You don't need all your photons to get to the destination. Only some of them. And you can use error correcting methods to ensure they have a useful pattern when they arrive.

If the errors are happening further out than your civilization has ever been, what's correcting them?

They are still quantum objects and still have diffraction and such.

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