Hello,
The native conversion doesn't update the TOC. Please check the information explained in a previous reply:
If you need to update the TOC automatically, you need to use a macro or the conversion plugin with the libreoffice or msword methods...
The native conversion supports a set of contents and styles (https://www.phpdocx.com/documentation/conversion-plugin/preparing-the-templates-for-its-conversion Supported OOXML tags and attributes when using the native method section). The DOCX you are trying to transform must be used some not supported content, please use the conversion plugin based on libreoffice or msword.
Regards.