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@Arkadian - things that I would consider/try
I would not be working within a calibre library folder, if I have to do a lot of editing on a book I prefer to do the editing outside of the library folder, mainly to avoid having files like Daniel Defoe - Treasure Island.1.epub, Daniel Defoe - Treasure Island.2.epub in the Library folders.
What happens if I make similar changes to File 008 and File 009 and then do a save, is the change to File 008 saved and the change to File No 009 not?
Is there any significant difference between the header for File 009 and and the other files? Can't imagine what, unless something like - <file disposition="read-only"> - exists in XHTML specs.
I'd try renaming and/or moving the File 009 in the file list and doing the edits and save.
BR
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