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Flight crew is only designed to catch gross errors. It is enough to try to keep up with editing function without trying to keep up with the moving target of validation.
Flight crew will catch most errors. But for a final check, all epubs need to be run through epubcheck.
Besides which, Sigil is a epub 2 editor, and merely doesn't mangle epub3s. Since there are very few devices which display epub3, and the whole field is in flux, it will be some time before epub3 will be fully supported.
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