You can run Indexer yourself, from the directory where your helpset file is located. To run Indexer directly from a .bat file, include the following commands:
REM The following command must be typed all on one line:
java -mx256m oracle.help.tools.index.Indexer path\to\hs myproj.idx
Paths should be absolute rather than relative. If a path includes spaces, you must enclose it (but not the parameters) in double quotes. Prefix options with a dash (“-”) rather than a forward slash.