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ATI Workstation Clone Changed Boot Sector & Windows OS Drive Letters

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I used ATI Workstation to clone my 64GB SSD to a 128GB SSD. Once the process completed, neither drive loads Windows 7 Pro. The Boot Sector is 100MB on both drives. But not it seems the Boot Sector is the C: drive and the Windows OS is on the D: drive (previously the Boot Sector didn't have a drive letter and the OS was on the C: drive). Assuming that's the case, how do I fix it so that Windows doesn't see a drive letter for the boot sector and sees the C: drive as the one with the OS installed on it?

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Yes, I'd found that same KB. Thought Acronis might have a quick fix rather than having to go into regedit.