An explanation and possible workaround has been provided by KayNeine here:
This certainly seems to tally with my experience and the hidden metadata theory does seem to answer why it could be happening. Just need Apple to acknowledge and address the problem.
As this Support Community obviously isn't moderated by Apple, can I suggest as many people as possible use the iBooks Author Feedback form to report their issues. Hopefully then, someone at Apple might take note and try and rectify these problems.
The link above is available from the iBooks Author App in the menu: iBooks Author > Provide iBooks Author Feedback.
Further to my earlier post we have now completed a test by saving our original document as a template, then creating a new document from the template, making necessary changes and saving as a new file. We can now upload the two separate versions to our iPad.
You cannot "duplicate" the file in any way, either by the File > Duplicate method from within iBooks Author or by simply Duplicating the original .iba file in the Finder, as this will cause the problem outlined above. By Duplicating you are obviously also duplicating this "hidden metadata" which is stored somewhere within the file which iBooks on the iPad is using to identify the documents. So unless Apple update the software to allow us to change that metadata we are stuck to using the Templates route. (Didn't have this problem on the last version of iBooks Author).
This works for what we are trying to do, which is create different language variants of the same book.
Working from Templates is probably the correct way to do it anyway, but might not necessarily be right for everyone.
Working in iBooks Author is proving to be a rather testing experience. You certainly need the patience of a Saint. Not sure it's of the standard we expect from Apple, but then I guess, as they are giving it away "free", they think they don't have to offer any support for it.
I think I would prefer to pay a fee for it and have a support route from Apple, rather than rely on a community of equally frustrated users who are all playing guinea pig and simply sharing their workarounds for a half baked product.
Good luck to everyone!!!