windows - Any harm in swapping SATA ports?

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)?