You must create a separate directory for compilation, then copy (do not move) the required files to that directory: .htm, .hhk, .hhc, .hha, and .hhp. Because the project directory contains a lot of other files that are all part of the conversion machinery, you must keep a set of these files in the project directory. Also, place your CSS file in the compilation directory.
Note: If you manually copy files to another directory for compilation, do not check Compile Help in the DITA2Go Export dialog; that option works only on files in the directory specified by[Automation]WrapPath (see §44.3 Understanding path values for deliverables). Compile from HTML Help Workshop instead.
You can use Windows copy commands to move just the compilable HTML Help files into place after converting a DITA document.
If you copy graphics files to the compilation directory, set the following option in project configuration file d2htmlhelp.ini, to remove path information from references to the graphics files:
[Graphics]
StripGraphPath = Yes
When DITA2Go finishes converting your document, select the .hhp file in HTML Help Workshop, and compile the project.