Material that DITA2Go converts to a JavaHelp 2 glossary no longer appears in the resulting JavaHelp 2 system as a regular topic. Therefore you might find an orphaned glossary entry in the JavaHelp TOC, pointing to a topic that contains only the original heading of your DITA glossary.
To eliminate a TOC entry for the glossary, do the following:
You must also remove any cross references to the heading from other topics.