"Could I perhaps have to re-run lilo after the links have changed where the links are pointing to? "
"If so, how would I go about running lilo? (tried from knoppix, (with -C) but it fails because of knoppix's read only file system - I would actually prefer if it did everything inside /mnt/hda3/boot, but I am guessing that's asking too much?'
In knoppix you can umount /mnt/hda3 and then mount it again as read write.
When you do lilo -C from knoppix you have to change the configuration information in lilo.conf to correspond to how the paths appear in knoppix. For example, suppose you do the following in knoppix:
mount /dev/hda3 /bootpart
cp /bootpart/etc/lilo.conf /bootpart/etc/lilo.conf.knoppix
Then edit /bootpart/etc/lilo.conf.knoppix and run lilo:
lilo -C /bootpart/etc/lilo.conf.knoppix
When you edit lilo.conf.knoppix you have to change the paths to reflect the way they appear in knoppix. For example:
image = /boot/vmlinuz-188.8.131.52.1-23-1-04
image = /bootpart/boot/vmlinuz-184.108.40.206.1-23-1-04
and so on.
Here is a lilo howto:
Be prepared. Create a LifeBoat CD.