After you set up your HTML Help project, you can choose whether contents and index will be generated by DITA2Go or by HTML Help Workshop, or by neither. This choice is governed by the following setting:
[MSHtmlHelpOptions] ; RefFileType = HHW (for HH Workshop), ; Body, or None (do not generate). RefFileType=Body
If you remove all settings for RefFileType from the HTML Help configuration chain, the default becomes RefFileType=HHW; therefore, if you specified that you want contents or index generated, they will be generated by HTML Help Workshop.
When RefFileType=HHW, DITA2Go removes attributes (including class) from <Hn> tags, and leaves the task of generating contents and index to HTML Help Workshop. You can edit the configuration file to change the value of RefFileType.
§16.3.1 Modifying contents or index production for HTML-based Help
§18.9.2 Generating contents and index with HTML Help Workshop.