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There's nothing about backing up with SD! that could throw a drive out of whack that normal usage wouldn't do too. We're literally just copying files -- we're just copying a log of them, quickly.
But if it's just vanishing, it's failing. It might be due to errors on the drive surface: you can try to erase and zero the volume you're backing up to... but if it's also not showing up in Disk Utility, I think the thing isn't reliable enough to consider using for backup.
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--Dave Nanian
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