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@Sefiriot--
Feel free. I'd be happy to discuss it with the Moon+ dev.
I originally assumed that the Moon+ reader was doing the same thing Sigil does--assuming unique file names and flattening the internal directory structure.
Going back and reading your description of the problem again, however, I now suspect that Moon+ is instead reading the first book's content.opf and toc.ncx instead of the master copies.
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