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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
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1 Answer

http://www.pugetsystems.com/labs/articles/SATA-cables-Is-there-a-difference-97/

Then they retested the results here

http://www.pugetsystems.com/labs/articles/SATA-3Gb-s-vs-6Gb-s-Cable-Performance-Revisited-183/

"The same cables and connectors used for current SATA implementations can be used to connect SATA 6Gb/s devices. SATA-IO recommends utilizing quality components to ensure data integrity and robust operation at the fast 6Gb/s transfer rate. Cables already at the threshold of 3Gb/s operating margins may experience lower performance than expected at 6Gb/s due to an increased number of resends."

thats a simple google search, so to answer your question, NO.. there is no harm in swapping sata plugs. hope that answers your question

edit for real question: Can I just swap the ports for the two disks, or will the operating system confuse them and think the WD HDD is drive E: now? (It has to remain drive D: or otherwise system will not work properly)

Simply, no it's not going to matter because, you're thinking about the old IDE days were the placement of the drive matters for HD boot order. These days its all controlled in BIOS. When you enter bios, theirs a section where you select the specific hard drive you want the computer to boot from. then in the actual BOOT order, you'll select Hard Disk-0 or the actual name of the hard drive is your primary or even secondary to your DVD-rom depending on your preference.

Normally to see this, start your computer and press DEL to enter bios, normally at the bottom of the screen it will tell you what button to enter bios.

As far as windows disk management goes, Each hard drive has a signature, and windows detects that signature and assigns it a Drive Letter, swapping the drive on your motherboard will not change that on Modern Motherboards with newer OS's like Vista/7/8 I can't really remember, but even win XP.

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Sorry, you misunderstood me I think, I am not concerned about the possible lower performance of 3GB/s cables compared to 6GB/s, it's about the SATA ports on my mainboard, 2 are 6GB/s, the other 2 are 3GB/s. The SSD on E: is currently connected to a 3GB/s and this cuts its performance (250GB/s instead of 500GB/s) in half. The WD HDD is in a 6GB/s which is of no use. Can I just swap the ports for the two disks, or will the operating system confuse them and think the WD HDD is drive E: now? (It has to remain drive D: or otherwise system will not work properly) –  Steve06 Sep 14 '13 at 11:24
    
Edit to answer your question, you should be much more clear next time on what exactly you're asking. Also, Don't be scared to test these things out for yourself, you'd learn a thing or two. –  Sickest Sep 14 '13 at 18:00
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