Well i have 2 SATA HDD's install and i can just go into my BIOS and turn off one or both of my frives. Neither is considered a master nor slave. I didnt have to mess with jumpers or anything. So if you do have 2 SATA HDD's installed you should just be able to transfer the data from the main 1 to the 2nd one and then format and reinstall.
I can hook up to 4 SATA HDD's on my machine and right now only to of the SATA ports are on. Check your BIOS and see if you can manually turn on or off your SATA like i can. But you will have to switch cables to do a fresh install.
SATA doesnt work the same way as IDE Master and Slave. My MOBO has "4 ports" to hook up HDD's. I turn them on or off manually. Since i can have 4 installed and running at the same time Master and Slave dont apply. It goes by the "Port" # that the SATA HDD is hooked up to. 1 being the main, 2nd being the secondary drive, 3rd being the 3rd drive and so on.
SATA does perform great. So if you dont have any info on your 2nd drive then just switch cables. Turn off the 2nd drive (Formally the main) and install windows again. Then after windows installs put the 2nd drive back on and then do a file and setting transfer.
I hope some o fthis helped. I had lots running thru my mind as i was trying to type this. If i am unclear or vague on some info just let me know i will post back with more accurate info.