Windows wants a Windows-compatible filesystem. If you have one already on there then it can be told to retain it. However, if that partition has a filesystem that Windows doesn't recognise then it will wipe it in favour of one that it does. Your best option is to move everything that's important off that partition before installing Windows on it. Also, Windows will most likely wipe your MBR. You may have to reinstall that after Windows is done installing. I recall you're running linux but I don't know what bootloader you're using. You will need to boot from the linux install CD and go to rescue mode.
Originally Posted by phantomcow2
Once booted into the rescue miniroot, here's how you would reinstall the grub bootloader.
Personally, I detest grub. You might want to check out XOSL. If you decide to use it, you would just install it seperately. Note that it requires its own seperate partition to live in. Also note that linux will still require a secondary bootloader (grub or lilo - I recommend lilo for this case) that should be installed into the primary linux boot partition (typically /dev/hda).
# chroot /mnt/sysimage
You might also want to install Ranish Partition Manager which integrates well with XOSL and allows you to modify and resize partitions.