I've never picked up at Chamartín, but I have dropped off at Atocha, and the procedure was utterly painless. It was with Avis, and they didn't even go check the car for "arañazos" [scratches].
As far as getting "there" [Chamartín] from "here" [Callao], if the 10 is down, you may be able to get there the "long way" on other lines. Taxis are always there...
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Ongi etorri!