Q: How do I move my System partition to a different disk?

A: I recently had this exact problem. Somehow my System partition (the partition the hardware initially uses to trigger the OS boot) was running on the wrong disk.

As you can see in the screenshots below, my F drive was the System drive but I wanted it on my C drive. (Note that ideally you would have a separate 350MB partition at the start of the disk, which would allow technologies such as BitLocker to be used in the future; however, it's not mandatory.)

System part

There are several ways to solve this however what I found to be the easiest way was the following using the Windows 8 boot media:

  1. Create a Windows 8 (not Windows Server 2012) bootable media.
  2. Shut down the server.
  3. Disconnect all storage except your boot disk.
  4. Turn on the server and boot from Windows 8 media.
  5. Select the language options and click Next.
  6. Click the Repair your computer link on the Install screen.
  7. Under options, click the Troubleshoot option.
  8. In the Troubleshoot screen, select the Advanced options link.
  9. Click Automatic Repair.
    Automatic Repair
  10. You might be prompted to select the OS to fix (depending on the scale of the problem); auto remediation will commence.
  11. The machine will reboot if it can be fixed. At this point, you might want to stop the boot, reattach the disks, and make sure you select the right disk as the boot device.

If this was a Hyper-V server, the hypervisor would be set not to launch, so you would need to run this command:

bcdedit /set {current} hypervisorlaunchtype auto

You can also check that the system partition has moved by using Disk Manager (diskmgmt.msc).

New System location