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When installing a new hard drive, I accidentally formatted it using 'Disk Management' and set it up as my primary active partition, even though it isn't the system drive. Then, when I restarted my machine, Windows wouldn't boot, citing a missing or corrupt SYSTEM folder.

How do I re-enable the system hard drive as my primary active partition? Any help would be greatly appreciated.

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Most computers allow you to manually select a boot drive. Usually after the computer posts, immediately after the BIOS screen. Consult your documentation on how to do this (although sometimes the keypress is listed in the BIOS screen). This would allow you to boot using your original drive and fix the problem.


Use fdisk or an equivalent disk tool to set the system partition as active, and unset the active flag on any data partitions.

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I can boot to either drive easily, the problem is the system drive has been changed to the secondary partition; and the newly installed hard drive as primary. – user32220 Mar 24 '10 at 19:52

What is the Operating System on the Primary Hard drive?

If it's Windows XP try booting from a startup disk (like Windows 98SE Bootable), use the FDISK command and choose the option to set the required parition ACTIVE.

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The OS on the system hard drive is XP. The new hard drive I just installed (and partitioned as PRIMARY) is empty. I don't have a startup disk? Do you mean something like my XP installation CD? I don't have anything like that unfortunately – user32220 Mar 24 '10 at 19:52
No, you can search for Boot images and burn it to a CD. look in – Srin Mar 24 '10 at 20:48
No boot CDs seem to work. I don't think it is recognising my system drive because I have changed the partition type, and made the new, empty drive the primary partition. – user32220 Mar 24 '10 at 22:48
You may need to change the boot order in your BIOS settings to place your CD drive above your HDDS, thus forcing your computer to attempt to boot from a CD rather than your HDDs. – Emory Bell Mar 25 '10 at 2:01

It sounds as if your BIOS is trying to BOOT from the "new" harddrive.

Try unplugging it, to see if that helps with your problem. In that case, try modifying the BOOT order in you BIOS.

Otherwhise it could be just normal wear-and-tear on the drive and it's begun to go bad. In that case you can try running harddrive maintenance utilities such as SpinRite

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Repairing the boot.ini file through the recovery console seems to have done the trick. I ran CHKDSK which fixed a couple of bad sectors as well. Thanks everyone for your help

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