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Hi Maia. Can you clarify something for us? Do you mean that you have duplicate files in your webhelp output and the duplicate files are in different directories? Or are the duplicate files in your RH project source?
Meant to say that you could try running the unused file report (available from the Tools > Reports menu in X5) to see if any of your duplicate files show up there. If they do, you can probably delete them.
In addition to what Colum offered, I would ask the following:
You say you have 6 or so help files that are essentially the same. Are you saying that you expected to have a single WebHelp output for 6 different versions of the help? If so, you should know that if all are about the same, you will indeed see 6 different sets of the files.
Do you have any Text-Only popups? If so, there will appear to be duplicated files. The WebHelp generation process creates a different HTML file for each popup. These files are a variation of the file name they are linked from. So if you have a file named Bob.htm, you may see a Bob1.htm, Bob2.htm etc. An additional file for each popup.