This is probably because you have two copies of your book on your computer with the same name. The other copy you have is probably in a cloud system (dropbox?)?. The thing that worked for me was to simply rename my book.
For some strange reason, iBook don't do this, and you can't do a lot of things in ibook that you should have been allowed (rename title if no title is found, or mixed up), but this is the stupidest mistake. Rename your file, and it will probably work.