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Well, technically, the file wasn't "perfectly good". The manifest in the .opf file is suppose to list every single file in the archive. So chances are, some files were sitting around that were not listed in the manifest.
Without the help of Sigil, you would have needed to manually look through the folders and make sure that each file was included in the .opf manifest list.
Of course, the question now is, what files did Sigil automatically discard, and did they include useful information?
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