Editio Self-Publishing discussion

I bought an elegant, format-heavy ebook template for a Kindle reference book. After one heck of a learning curve so far, I have everything working with the huge exception of the NCX that KDP's conversion software generates. I'm getting multiple duplications of chapter and heading titles in the NCX. I've followed the Smashwords Style Guide instructions on avoiding this, to no avail. Is there some way to publish on KDP without a NCX?? The book has a detailed linked TOC, so the NCX seems superfluous....