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You may not want to enable Delete Files not in Manifest if you have (or if you're concerned about having) a poorly-done ePub file where important files (like CSS) may be referenced in the HTML content but not in the manifest.
You may not want to enable Replace Content Language Code if you don't have hyphenation enabled and you don't have any problems related to language formatting (hyphenation, etc.), or if you don't have the correct language defined for every book in your calibre library.
You may not want to enable Smarten Punctuation if you don't like the fancy punctuation marks.
You may not want to enable Clean ePub Markup if you want to keep cruft that Microsoft applications insist on inserting, empty heading tags, self-closing paragraph tags, or Unicode replacement characters (�).
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