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Could you describe an example a bit more - before after entries in the TOC, and explain how a heading gets removed?
Its something I can add to the issue log to track.
In addition to modifying Generate TOC to add the ability to select the heading levels to include in the generated TOC, I've though about using regex to search the document for certain patterns, possibly even entries already in TOC, and then allowing you to choose which entries to include. That would allow auto-renumbering, but is a much bigger issue that may not be as useful.
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