If you provide mid-topic links in the TOC, you lose contents tracking of your current location in the Help system. And if you specify a binary TOC in HTML Help Workshop (which you must do to enable certain HTML Help features), mid-topic entries in the TOC become relatively useless. These are known HTML Help problems; DITA2Go cannot fix them.
Why not to include mid-topic links in the TOC
Providing mid-topic links in the TOC is generally not a good idea, for the following reasons:
No binary TOC with mid-topic links
If you specify a binary TOC in HTML Help workshop, and you have mid-topic links in the TOC, the name of the last TOC link to a given topic file becomes the name of all links to the file, unless you use the following settings for all but the first heading:
[HTMLStyles] Midtopichead=Contents NoContLink
However, with this setting the mid-topic entries are no longer active links, which is likely to annoy users.
If you must have mid-topic links in the TOC
If you are willing to give up synchronization to get drill-down, and your project does not require a binary TOC, do the following:
[MSHtmlHelpOptions] ; ContentsNamesFileOnly = Yes (default, allows tracking) ; or No (allows direct mid-topic jumps to points within files, ; but disables tracking) ContentsNamesFileOnly=No
TOC entries reference points inside .htm files (that is, the links have #place suffixes), so you can drill down into the file via the TOC; but TOC entries no longer synchronize with topic content.