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I have 3 disks in my desktop PC (Z77 Intel Ivy Bridge chipset with 2x SATA 6gb/s, 2x 3gb/s ports). Current disk / drive letter mapping:

Drive C: | SSD Intel 530 Series | Main Windows 8 drive

Drive D: | HDD Western Digital 1TB | User accounts

Drive E: | SSD Intel 520 Series | Windows swap file

C: and D: are on 6gb/s SATA ports, while E: is on a 3gb/s SATA port.

I am aware that 3 and 6gb/s transfer speeds are not realistic anyway and more of symbolic nature, but using the "Atto" SSD benchmarking tool I could see that drive E: actually only runs at half speed (~250 GB/s instead of 500 GB/s), which is why I'd like to swap SATA ports.

The boot order would not need to be changed as drive C: and the corresponding port would not change.

However, I am concerned that after swapping the SATA ports on the mobo between D: and E: they might be confused by Windows (e.g., Windows looking for user account data on the Intel 520 SSD instead of the Western Digital hard disk).

If I am right, how can I possibly re-map the drive letters before booting up Windows (and risking to corrupt it)?

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If you change the port number then you have to verify the boot order. What is your question exactly? – Ramhound Sep 14 '13 at 2:41
3Gbps SATA is limited to 300MB/s due to its 8b/10b encoding overhead. That's theoretical max - 250MB/s isn't unusual for a practical limit with other overheads. – Bob Sep 14 '13 at 2:54
@Ramhound: Boot order should not matter because the boot drive C: would remain at the same port. I'm asking about switching ports D: and E: and whether the disk to drive letter assignment would change if I swap the ports. – Steve06 Sep 14 '13 at 11:26
@Steve06 - Even if they did change you can change them by hand. – Ramhound Sep 14 '13 at 12:52
That's the thing. Windows' Disk Management may not be an option if Windows fails to boot up properly b/c user account data is stored on drive D:. Therefore, the question is whether I can change drive letter before starting Windows, with some Boot CD. – Steve06 Sep 14 '13 at 15:05

It's fine. You won't corrupt anything. Worst case scenario you swap the ports back the way they were.

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If you had a RAID setup I would say yes, swapping the ports is not recommended. Switching the ports on a Windows based machine does not matter AFTER it has been assigned a drive letter. If you swapped the ports before assigning a drive letter then the drives would show up in a different order in Disk Management. (I.e. drive A could be drive 0 and drive B could be drive 1 and a port switch could swap those). On your motherboard, the SATA ports are usually colored and labeled with numbers from 0 to N, N being any number. If you change the ports across different colors that means you are changing hard drive controllers. You may not want to do that in a system that the drive depends on the type of controller it's on.

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There is a way to use GRUB (GRUB2) to assign the drive letters prior to loading windows.

GRUB is a bootloader. There are other bootloaders, but I am most familiar with GRUB.

You can also solve this problem using virtualization. You can virtualize your Windows setup such that your machine boots to a bare metal hypervisor such as Xen, or you could use Ubuntu or even a fresh install of Windows as the host, then load your virtualized system from any hard drive. In this way, you can preserve your setup and at the same time liberate it from physical constraints. The details of how to virtualize your Windows setup is beyond the scope of this question and have already been well documented, so no need for me to rehash it here.

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sounds like an overkill :) – Anthony Jun 6 '15 at 7:19
Yes, these are two possible solutions and GRUB is the simpler solution so probably should be listed first. I will edit it. – user322404 Jun 9 '15 at 12:07

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