Open a project (.hhp) file, click Change Project Options, and then click the Compiler tab.
Change Project Options
Specifies files, compiler, window, and other project settings.
Select the Don't include folders in compiled file check box.
Notes
This procedure consolidates your compiled help file by removing all unnecessary references to folders. All URL references in the project are updated to reflect the new file location.
File naming is important when using this feature. Files in different folders that have the same name will not compile properly when consolidated at the root.