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The nails will only rip the belts if they are really proud of the surface, like 3 or 4mm. The sander will take down the heads of the brads as you sand, and give them a nice flush finish. You need to check that all boards are creak-free by walking up and down all of them before sanding. I left a single board screwed down so that I could get access later (countersunk pozidrive screws).
Did you chaps use a punch to make sure the nail heads were below the surface before you sanded, or did the sander take the nail heads in their stride?