@BelgarionNL - I think your issue now is that while Find Duplicates can automatically remove binary duplicate formats, you're left with all the book entries with no book formats (ie. book files) attached. You'd like to delete all those empty book entries because they're duplicates of their matching book entry. If that is your problem, I have a solution.
Add a custom field "format". It's a standard custom field so real easy to add.
Choose to display that new field in your book list.
Now you can see which books have book formats and which don't (because FindDuplicates nicely removed them for you).
Sort by format.
Now you can select and delete all the book entries with no formats real simply.