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Sigil only ever builds its toc from the contents of the heading tags h1, h2, h3, etc.
So whatever you have done has changed the contents of those tags in some way. If you want to override a heading tag you can set a different string in that tag's title attribute. This can be made easier using the TOC Editor.
Without specific examples of changes to those tags and to the resulting toc, there is no way to help.
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