DITA2Go creates a helpset file for you the first time you run a JavaHelp conversion. Although DITA2Go rewrites .jhm and .xml files every time you run the conversion, by default DITA2Go does not rewrite the helpset file during subsequent conversion runs.
To have DITA2Go rewrite the helpset file every time:
[JavaHelpOptions] or [OracleHelpOptions]
; WriteHelpSetFile = No (default) or Yes (write each time)
WriteHelpSetFile = Yes
Set WriteHelpSetFile=Yes if you move or delete the helpset file from the project directory every time you run the conversion.
Use the default value, WriteHelpSetFile=No, if you customize the helpset file outside of DITA2Go; see §20.3.7.5 Adding custom helpset sections for JavaHelp 2.