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I have an epub with dozens of errors of type 'link target is before the previous link’s target in document order.'
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Typically this is an NCX or Nav issue where spine order and the order used n the nav/ncx is inconsistent. It can be as simple as having one link out of order.
The solution is just to rebuild the TOC from the original h1-h3 tags if possible. Ids themselves are not numbered but in the nav and ncx the order must match the playorder, (typically the same as the spine order of the files).
In fact the playorder attributes are not needed anymore.