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What was their reason and how much did they take off?
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If it was just to correct ridges and not warpage, the amount taken off is minimal and will not cause an issue, while the brakes may get a little hotter, it is probably so little it is not even measurable. The disks are designed to be thick enough to be skimmed a couple times before needing to be replaced.
I am quite sure this will cause no problems and if it was mine I would rather have seasoned disks that have been skimmed rather than new. Seasoned disks have already seen a lot of heat cycles and actually perform better and are less likley to warp than new disks.