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I am not sure what your two .opf files contain, but the EPUB 2.0.1 specs www.idpf.org/doc_library/epub/OCF_2.0.1_draft.doc (section 10.1) say:

The <rootfiles> element MUST contain at least one element
that has a media-type of “application/oebps-package+xml”. Only one
element with a media-type of
“application/oebps-package+xml” SHOULD be included. The file
referenced by the first element that has a media-type of
“application/oebps-package+xml” will be considered the EPUB rootfile.
The EPUB rootfile (the OPF package file) MUST NOT be encrypted.

This means that you can have more OPF files in the container, and even reference them in the container.xml, but only the first will be considered the primary one. (And, I add, most real world reading systems will ignore the others.)

Note, however, that you can have multiple renditions inside the EPUB container:

<?xml version="1.0"?>
<container version="1.0" xmlns="urn:oasis:names:tc:opendocument:xmlns:container">
<rootfiles>
<rootfile full-path="OEBPS/My Crazy Life.opf" media-type="application/oebps-package+xml" />
<rootfile full-path="PDF/My Crazy Life.pdf" media-type="application/pdf" />
</rootfiles>
</container>

So, just having another OPF file is fine, as long as you list it in the <manifest> (of the OPF actually referenced in the container.xml). For any functional purpose, it will be ignored by the reading system.

Comment 1: I still think that the EPUB you have been given is probably the result of some sort of experimentation, and having two OPF files is the result of some mistake.

Comment 2: in theory, having multiple OPF files is a way to pack multiple renditions of the same publication inside the same EPUB container. The IDPF has a working group on multiple renditions: www.idpf.org/epub/renditions/multiple/


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