When you create a folder in RoboHelp, the FPJ is part of the XML structure used by RoboHelp to manage and track topics. I would think RoboHelp will become awfully confused and project corruption will ensue if you start deleting FPJ files.
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Like Rick said doing that would cause confusion.
Because RoboHelp maps references for each topic/htm file in FPJ file. So, assuming a Folder A has ten topics, FPJ inside A would have XML structure for all 10 topics, if FPJ is removed from A, in Robohelp Project manager, you would not see any any topic listed, even though it would be there at source.
yeah, I tested it anyway in a copy, and the destruction was wonton and wide-spread. So, I have been editing the fpj files manually - easy, but tedious in a very branch-y file structure. Too bad there isn't a reindexing utility that could just reinventory all the contents of a folder and reupdate the fpj files. But we are pressing on - one domino down, many more to go!