How did you mark Chapter headings in your Word doc?
Suppose you had styled them with the Word built-in style 'Heading 2', then when you Saved-As Webpage-filtered the Chapters would be tagged with <h2>...</h2> tags.
Then after importing the html into calibre you would run a conversion ZIP to MOBI, with conversion settings:
Convert - StructureDetection - Detect Chapters at: //h:h2
Convert - TableofContents - Level 1: //h:h2
This would create a single-level metadata TOC (in file toc.ncx) in your MOBI. Nothing at all to do with the inline one you already have.
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