No not syncing with anything. And I don't think I'm using a virtual library.
The library folder structure look exactly like you describe it and how it is supposed to be.
At the moment I don't have an example of a book that is missing (that I know of) When I find one I will update this post with what I find in the metadata file.
Metadata.opf file seems to fine for the missing books.
Last edited by Corwyn; 11-18-2014 at 06:07 AM.
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