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Originally Posted by JSWolf
When you convert ePub to Mobi, the NCX gets converted to a linked ToC that is at the back of the Mobi.
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By what software?? Kindlegen certainly doesn't create a "linked ToC at the back of the mobi" from the NCX file. Nor does MobiPocket Creator. Calibre will do it if you
tell it to, but it's quite easy to check the box that will stop that behavior.
You might be the one that's confused here.