Since the partition created its own partition to store the image file, it may of changed how the linux partitions should be referenced. Since you said it is a secure partition, it may be of an unknown type that looks like it is empty.
If your system boots with grub, you can try to select the kernel manually. The grub shell has autocompletion, with makes it easier to use. Another option is to boot with a live distro, or your rescue system and see what the partitions look like. Finally you will need to chroot to your system and correct your fstab file, and either the /etc/lilo.conf or grub's menu.lst file.