You are making the change from within Windows, but it's actually modifying the DVD-ROM/DVD burner's firmware. Thus, you can set the region of each drive seperately, setting one does not affect the other in any way, and if you ever replace the drive with a new one, you'll be starting out fresh with 5 region changes.
Hope this helps,
P.S. Don't forget, you can send the drive back to the manufacturer to have the count reset so you can change the region code again. However, the manufacturer can only do that 4 times per drive.
I have a DVD drive and a CDRom drive in my tower and I am thinking of swapping out the CDRom drive and replacing with another DVD drive that I can use for reading different region discs. Once the region setting becomes permanent, does this only affect the drive? For example, if my original DVD drive stays region 1 and I change my new DVD drive to region 3, the new drive's region won't affect my original drive correct?