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I had a similar problem as mentioned earlier, with KFX conversion removing ToC completely. I managed to solve it, so I'm posting this as I don't think anyone else has posted a solution.
After trying autogenerated ToC, removing ToC completely before conversion, etc. (nothing worked) I noticed the book had longish names for internal content files, with spaces and whatnot. As a symptom something was wrong, the log had a lot of lines about removing anchors from ToC entries (essentially links to those content files). After bulk renaming the content files to something short and simple like "Part-n" ToC was there after conversion to KFX.
I don't think it's in any way plugin's fault - opening the problematic EPUB directly in Kindle Previewer also ate up the ToC. Of course if it would be possible to figure out what exactly is KFX problem with long filenames (or maybe it's the spaces that were the problem), and rename them on the fly if needed, then it would be just great.
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