I wonder if it helps you to know that Windows-xp has a repair function. If you run setup and press the right choices you can let Windows install itself in repair modus. I had to do this once before and it went very well, I got everything back. - Of course I don't want to give you any guarantee here because each case might be different, but even for a new installation, I would not expect Windows to overwrite application data - unless you choose re-format or re-partition.