You'd have to take a look at the code (which you can do selecting the html files in the drop-down list next to "CSS files" in epubutils.py) and see what is used for Chapter 1 (maybe <h1>Chapter 1</h1>), what for Headings (maybe <h2>Headings</h2>) and what for Sub-heading (maybe <h3>Sub-heading</h3>). Then you should modify the CSS rules passed to prince accordingly, by adding "prince-bookmark-level: none;" to the elements you don't want in the TOC.
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