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Internally, we use Disk Utility to erase the drive, so there's no real difference. However, once you've put a backup on a drive, we keep track of it using its low-level ID, which is assigned during erase. Erasing outside of SD will cause us to lose track of the drive, so you'll be prompted to select it again.
It's a good idea, with a new drive, to zero it out. That way, any low-level defects will get remapped.
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--Dave Nanian
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