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Since Stanza is primarily an ePub format reader it is more than likely that these are ePub format books encapsulated in a Stanza shell to provide the reading facility. Nothing you said contradicts this assumption. An ePub book is basically a Zip file with a standardized set of files inside.
It might be worth taking all the files, zipping them up into a single file, and then changing the file extension to ePub and see if Calibre (or an ePub editor like Sigil) is happy with the results.
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