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Are the missing section headings generated through InDesign’s TOC “Title” field, or are they ordinary paragraphs? One useful test would be to put a dummy heading in a separate, ordinary text frame, apply one of the missing headings’ paragraph styles, and export a copy. Does that heading appear in the NAV TOC?
Could you also share a screenshot of the EPUB TOC style’s “Include Paragraph Styles” list and the export dialog’s “Navigation TOC” selection, with private information removed? That would help narrow down whether the issue is with the selected TOC setup or those particular headings.
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