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You don't need to delete the book entry in calibre. Select the book in the main window, click 'Edit meta information'. In the top right of the Edit Meta Information dialog is 'Available Formats'. Select the format you want to replace, click the trash can to remove that format. Click the 'Add new format...' button (book with +) to add the new version.
That should save you a little time, and retains cover/metadata information.
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