Clonezilla hard drive clone - Target HDD not booting

[Armand]

I am tasked to clone an IDE HDD from an industrial computer. The HDD has on it a Windows 2000 and MS-DOS partition. I want to clone the entire disk to another IDE disk of identical size.

The original HDD presents a boot menu prompting for which operation system to use, Win 2000 or MS-DOS.

I removed the source HDD in question from the computer and ran Disk Part => Clean on the target HDD. I have the two hard drives connected via a IDE-USB adapter to a workstation computer via USB.

I decided to use a Clonezilla live USB to clone the source HDD to target. I want a bit-for-bit clone of the source because I don’t want to mess around with bootloaders and whatnot for the two old OSes (Win 2000 and MS-DOS). I was under the impression that Clonezilla did this but I could be wrong, because I ran the disk-to-disk clone in easy mode, went through the clone successfully and was not able to boot the newly cloned HDD in the source computer. Upon attempting to boot the target HDD in the source computer as if it were the source HDD, I get a “could not find boot partition.”

Granted, Clonezilla did prompt to copy over the MBR of source HDD and I did so, but I was hoping that this would be a clean bit-for-bit clone, kind of like how a scanner scans a paper.

What am I doing wrong here? How can I get a clean bit-for-bit clone? Thank you.

[Steven Shiau]

For disk to disk cloning, yes, it will clone the boot loader, too.
However, is your destination machine different from the source one? If so, your MS Windows might not work.
BTW, you can use MS Windows installation disk to fix the boot loader if Clonezilla really fails to clone that for you.

Steven