Extract the index.xml
unzip Filename.iba index.xml
Edit your index.xml file as you see fit (like changing the GUID: http://www.reactuate.com/2013/03/21/ibooks-guid-problem-when-duplicating-ibooks-author-documents/)
Remove the original index.xml entry from the .iba file
zip -d Filename.iba index.xml
Re-add the modified one to the end, with the proper compression (assuming modified index.xml in same dir as Filename.iba)
zip Filename.iba index.xml