IMHO, this is mostly a cosmetic problem for users with slight OCD tendencies, because a properly designed ePub3 book with an .ncx file, can be opened even by the oldest ADE version, because the reading system is supposed to ignore unknown tags.
If a book only has a navigation document all you have to do is generate a TOC with Sigil and export it with the ePub3 output plugin.
If the book didn't have any validation issues other than the issues caused by down-converting it from epub3 to epub2, you'll end up with a valid ePub3 book that can be read with either ePub2 or ePub3 apps.
As for JavaScript, SMIL etc., you can ignore them, because they won't be supported by ePub2 apps anyway.
Last edited by Doitsu; 12-14-2015 at 01:08 PM.
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