For multiple books, select several books and right-click on the selection. One of the menu choices is "Remove Books". Then you have more choices, one of which is "Remove files of a selected format from selected books".
You can do this for a single book as well, or go into Edit Metadata, and in the top right corner, select a format and hit the "Remove the selected format from this book" icon (lower right icon of the four in that corner).
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