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As I mentioned once before, adding in soft hyphens should be the very last step when producing an ebook and only done if the targeted downstream platform supports it.
I recommend using search and replace to remove all soft hyphens first. Then build your epub, tweak it to your hearts content, validate it, and then as a final step use a hyphenator to put soft hyphens back if you truly need them.
As DiapDealer says, we will look into excluding the nav from index creation, but you can always edit the index after creation.
KevinH
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