If your HTML files will not be in the same directory with toc.xml and idx.xml, links from these files must include a path.
To supply a path for contents and index links, and also for <context> elements (see §21.7 Setting up CSH for Eclipse Help):
[EclipseHelpOptions] ; TocIdxFilePrefix = prefix to insert at start of file URLs, when ; html files are placed in a subdirectory under the toc and idx TocIdxFilePrefix = path/to/htmlfiles
The path specified by TocIdxFilePrefix is relative to the directory where toc.xml and idx.xml are located, and must designate a subdirectory under that directory.