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The only way you could probably damage the cable is by trying to force it incorrectly, even then, you'll probably damage the drive and not the cable.
Always remember, the red (colored) stripe goes closest to the power connector.
As for the CS/M/S, I always manually set them to M/S and put them anywhere on the cable I want. The positioning on the cable doesn't matter if you use the M/S jumper.
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