Do I understand you right, that sda is your main disk and sdb is your backup disk?
Then it is as simple as that: Zero out the partition table of the second disk, you can do that in the running system. Just do
Code:
dd if=/dev/zero of=/dev/sdb count=1 bs=512
Make sure that the drives are really in that order before you launch this command! It will zero out the partition table of drive sdb!
If you now reboot your system will start completely from sda and you can start the backup.