Have you ever tried Sigil? I find it much better than Calibre for this purpose. I've only once or twice ever been obliged to look at the NCX file in a Sigil epub, and I've never had a validated Sigil epub give a problem when uploaded to the KDP. (I don't use KindleGen or Kindle Previewer for this purpose, and indeed have never been able to get KindleGen working on my Windows 7 desktop.)
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