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Take some of the books in the weird folders and add them to a new empty library (create it with the same structure as the old). Examine the books there and save to disk from there and see if you can reproduce it.
If you can't reproduce it then your library is corrupt. The library maintenance tools may fix it.
Or make a copy of a book with the problem and post here.
You can't post a copyrighted book so you have to use a public domain book and transfer the problem metadata to it:
Work in the new test library (so you don't delete the real book!)
I believe you can use a public domain epub book and simply drop it on the details pane. Then it should replace the existing epub or add a epub format book to the title. Save to disk again to write metadata to the epub and post here...
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