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ok - hierarchical is because you have a mix of h1, h2 & h3 tags. the calibre viewer indents to show/hide the sub headers..
what to you see if you look at the mobi with the same calibre viewer - I'd expect to see the same structure.
NB kindle navigation does not jump to H3 tags, only to h2 ( & to H1 I expect)
check if your minor headings are h3 that could explin whey the are lost in mobi
you can easily change h3 to h2 in Sigil because Sigil will take care of matching end tags
so just find <h2
replace with <h3
in Sigil code view across all documents should do the trick.
as always, take backups beforehand.
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