These are the instructions to make a cloned drive bootable again if the original had bad sectors. These instructions are only applicable for any Windows that uses the BCD, which is Vista and beyond, and has a MBR. You will need a Windows 7 or later DVD or equivalent USB stick; a Windows Vista disc will be harder. This assumes that the OS files were cloned successfully.

• Run chkdsk on all the partitions.
• Identify which partition has the BCD files. If there is a recovery partition, chances are good the BCD is stored on that drive.
• Use the following commands in the diskpart program:
• LIST DISK (use this command to identify the cloned hard drive number)
• SELECT DISK # (where # is the cloned hard drive number)
• LIST PARTITION (use this command to identify the partition with the BCD files)
• SELECT PARTITION # (where # is the partition with the BCD files)
• ACTIVE
• EXIT
• Now run the following commands: (Of course, some are redundant!)
• bootsect /nt60 sys /force
• bootrec /fixboot
• bootrec /fixmbr
• bcdboot d:\windows /s c: (where d:\ is the drive letter with all your Windows files and c: is the system partition from above)
• NOTE: Usually but not always the system partition is given the driver letter c:. If it was not given any drive letter, you will have to use the diskpart commands to assign it a drive letter. But it some cases it may not be c:, in some cases it may be on the same drive as your Windows files.
• Reboot.
• If problems still persist, run startup repair.