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Hard Drive Clone or Backup and Restore?

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This is why I suggested to do the BACKUP, not cloning.
Time is running out. And if something goes wrong, you may need to recover the entire system from scratch. Unplugging drives and putting them into caddys firstly can potentially damage the HDDs and secondly would work slower than plugging the second hard drive to the PC. I wouldn't touch the partition sizes for a simple reason - some computers won't boot after changing the partition size.