Eeesh, so you've copied both the 40 on the iBook and 40 on the external to the same partition?
OK: as long as you know what the existing 40 was, create a copy script. In the first tab, enter a description (might I suggest "This script is designed to un-screw me."
). In the 2nd, include "Backup - all files". And, in the 3rd, add the folders that you want to IGNORE (not copy) to the partitioned iBook.
Once that's done, save to an appropriate filename and use that, with Smart Update, to copy back to the iBook. I think that'll work.