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Doesn't matter which version you use. Sigil will change the file structure to the standard, this was also the case in the old version. If the file structure is different in the original, it will generate a problem. I assume that the ePubFixer will extract the opf and/or ncx and afterwards reinsert them into the epub. if the filenames or locations have been changed, the opf and/or ncx are no longer correct and thus resulting in the errors like above.
The advise from theducks is sound. I would open the file in Sigil 0.4 and manually correct the ncx and/or opf there.
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