I'm having the same problems, with a little difference. I just finished building my dedicated Linux box, and I want to free up the HDD space for WinXP on the 2nd HDD. I have WinXPpro on one HDD, and Mandrake 9.1 on the other.
I tried deleting the partitions, but as soon as I reboot the computer, it imediately gave me an error about the boot-loader.
I tried unplugging the Linux HDD, and got the same error.
To get it back up and running, I had to re-install Linux on the 2nd HDD can anyone help point me in the right direction?