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My point wasn't that you use the GUI in general, my point was that you use the GUI once to see all the ebook-convert arguments that get used from the GUI. If you set all the same cli arguments that are used in the GUI then you should get the same results as the GUI using ebook-convert. Once you've got the arguments right you can go to town with whatever scripts you want to use.
Note the GUI can also batch convert any number of books, FYI.
If that bug-fix you mentioned was related to your problem then the latest version of Calibre on the download site would already have that fix.
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