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The font settings are saved in two places. When you change them, they are saved in the database for that book. Reopen the book, and you have the same font setting as the last time you opened the book.
The settings are also saved in the config file. When you open a new book, these are the settings used. They will also be used for any book that doesn't have saved settings.
Personally, I wouldn't worry about it. If you have the perfect settings, then anything you read from now one will use these. If you reopen a book with saved settings, then you can fix them then. If you really want to remove the settings, you can use calibre and my Kobo Utilities plugin. It has function to change or delete the font settings. Otherwise, you can use an SQLite database manager to delete the saved font settings. Or removing these books will also clear their font settings.
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