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After eyeballing the code, there is one code path that could result in a possible missing spine close tag. So would you please copy and paste just the epub2 original content.opf here so I can try to see how that code path actually gets triggered and find the bug if one exists.
That is assuming that epubcheck is okay with the original epub2 opf. Otherwize the plugin is bound to have issues with a broken opf.
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