I admit I don't know anything about LiLo, but with grub it installs in the master boot record and the configuration file lives in my /etc/grub.conf on my Linux partition. I accidently deleted my Linux partition and thus the grub.conf. My system would not boot. I went to http://www.bootdisk.com
and downloaded a disk image for Windows 98 SE and booted with that disk and ran FDISK /MBR to clean out the master boot record. you must use the /mbr switch or you will go into the fdisk menu. then removed the floppy, rebooted and WinXP was happy again. I then re-installed Fedora.
Hope it helps,