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I don't know much about lasers, but this seems a very "dirty" environment for that sort of thing. Wouldn't the lenses etc get all fouled up?

your beam waist is going to increase (and intensity is going to drop) after a few hundred meters. you'd have to lower the whole laser down the hole

Maybe use adjustable lenses?

That's what adjustable diopters are for. Also, at certain power levels, the beam is self-focusing.

Dust? Vaporized rock going through a vacuum is not going to be kind to the inside of that vacuum.

Yes, this is a known thing to anyone that does stone engraving for a hobby. Those are then considered consumable parts in the operation.