Hi Jackie,
Thanks for your interesting suggestion!
I have looked into the <spine> section, but unfortunately found no duplicates, just every chapter (starting with chapter 2 or 5, depending on the book) once. What puzzles me is that before the spine section, the chapters are already enumerated in the opf file, but not starting by the first chapter (e.g. 2 or 5), but for example by chapter 10.
Knowing just a tiny little HTML and this kind of language, the content of these files seem pretty complicated to me, so I can't tell what entry or maybe what little symbol may be causing the error. After seeing how much code there is just as the book's "skeleton", I wouldn't be surprised if my problem would result from just a tiny mistake in these lines of code.
I can tell for sure though that the chapter ids aren't duplicated.
Thank you very much for your input, it made me navigate a step further into the depths of an ebook file