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KindleGen does that sometimes. It's one of the bugs that shows up to bite you*, especially if the <text> of the chapter title includes both a colon and an apostrophe in it.
My workaround for it is to create a final "dummy" <navPoint> entry which can go to any chapter for the href, as long as it's got a unique id and has a playOrder following the actual final chapter.
The trick is to leave the <text> for the dummy final chapter completely blank, which will keep it from being incorporated into the NCX, but usually manages to "force" KindleGen to create a functioning NCX point for the real final chapter it tried to skip.
Hope it works for you.
* One of these days I'm going to have to assemble and post the list of KindleGen's wonkier "features" and how to get around them if it's at all possible from the stuff I've tried.
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