This may be a stupid question, but if I were to do a clean install (as I may have to do since I've now went 4 times trying to do an upgrade install with it BSODing right when it's about to finish...two wasted hours), and I backed up my files to my D: drive (C: is my master, D is slave), would they still be deleted, or would they be fine?
As long as you leave the partition or drive alone with your backup you will not lose your backup. I do NOT use partitions so when I'm about to do anything that can wipe out my backup I simply unplug the power to the backup hard drive so that the system can't find it and won't possibly delet it.
Here is the risk.... I'm running my OS on drive c: but when I boot from the install cd and go to the command prompt my drive c is now my 3rd hard drive because that's the order my system sets up my hard drives. I have to be VERY careful about formatting or fdisk (disk manager) because c: is now my backup.
You'll find dozens of "help me" messages here from people who have partition problems.. mostly because the install placed the boot files on another partitoin.... and when they formatted that partition they couldn't boot... even though their entire OS is still intact. They either have to reinstall or learn how to recreate the boot files on their C: drive.
My advice... backup your MOST important stuff to a dvd or pen drive. You can get a 32 gb pen drive for about $15 from eBay... it's slow but it works. Or you can get a huge hard drive for about $50 and just install Win 7 to it and leave your backup alone.