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Is the problem that BD is not "remembering" the Book Cleaner settings (ie when you run BD and select "Tools/Book Cleaner", has it "remembered" the two file settings?), or that it doesn't appear to be "doing" anything?
Book Cleaner only does anything when you load a new file into BD; it doesn't do anything when you open an existing BD file, or if you "paste" content into a BD window; you have to actually open the new file, either using the "File/Open" button in BD, or by right-clicking on a file in Windows Explorer and selecting "Open With..." then "BookDesigner".
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