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Hmm, I guess for epub3, the DOCTYPE might not be as important since no quirks and no named entities but for epub2 it really is required for xhtml to technically work properly.
That is why I added looking for it to the well formed check in Sigil. On ImportEPUB the error message for not well-formed was expanded to include it for Sigil 1.4.0.
Did you try looking at all the warnings from epubcheck to see if at least a warning is generated?
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