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These websites might help you with how cloning works.
When to image a hard drive, and when to clone it | PCWorld
Disk cloning - Wikipedia
As I understand it cloning copies the hard drive into one big file. That file then is written to the new disc in much the same way as any software program is. In other words it's not the same as copy & paste. It's not actually coping sector by sector, thereby removing the bad sector problem being transferred.