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Reinstalling will have no affect on any work in progress, Tom. Particularly if the project and source files are on another drive.
One thing that I'd do is back up your Documents and Settings folders, just in case.
With your Media and Projects on your other physical HDD (it is a
) HDD, not a partition, right? If it is a partition, then do a complete backup of it - maybe even two: a set of DVD's and a copy to an external HDD, maybe by Ghost, or similar.
If you had a rootkit virus, I'd go so far as to do a low-level re-format of the HDD, then format it NTFS, prior to installing the OS and your programs. Depending on the type of HDD and its connection, the directions for a low-level re-format will differ. Your mfgr's Web site should be able to give you info and directions to step you through. You many have to download their utility and include it onto a bootable CD/DVD.
Get all of your install disks at hand, and make sure to make hard copies of all of your keys, and S/N's, that you might have scattered about on your machine. Also, make a backup of ALL programs that you installed from a download.
It might be well worth your time and $ to pick up an external, that can hold whatever you have on your system.
Little is worse than doing a complete re-format, only to realize that you no longer have the install keys, activation keys, and any downloaded install files, 'cause they are now history - gone to byte heaven. Even CSI could probably not recover that data now. Oh wait, they have a magic powder, that when applied to the platters of a HDD will reveal all of the 1's and 0's lined up perfectly - I saw that on TV once! [just kidding]
Good luck and do all of your planning before you do anything,
Yes, my secondary drive IS a physical drive, not a partition.
Actually, I picked up yet another 500 gig SATA drive for $70 ..
just in case.
I might do a re-install on the new drive, & wipe the old one
when I'm satisfyed that all is re-installed correctly & working.