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The fpj file is a folder file that contains a record of all the files that are located in it. Each time you add, delete or rename files the fpj file is updated. It sounds like this file has got out of sync with what is actually in the folder. Assuming that you have no files in the folder, open up the fpj file in notepad and see what is inside it.
This is what's in the .FPJ file:
<?xml version="1.0" encoding="windows-1252"?>
<rhpml majorversion="1" minorversion="0">
Have you saved your project?
Yes, I've saved the project repeatedy. I should say that I imported a Word file to get this folder, then in RH copied the files from the imported folder to another folder, and now I'm trying to delete the imported empty folder. I think I just need the right combination of steps to do it. Worst case scenario is that I keep the empty folder in my project, but that's a hassle for version control.
RoboHelp is re-creating the folder because it believes it is needed. This could be an arduous process figuring out why. Often, as you have noted, it is a result of bringing content in from Word. Scrutinize the documents you brought in that may be related. Specifically, look at the HTML code. There has to be some reference somewhere (whether it is valid or not) that is causing RoboHelp to consider the folder should be there. Once you ferret out where the reference is and squash it, RoboHelp should allow you to delete the folder. But as I said earlier, it will probably be a fairly long process.
First, a cup of coffee!