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Better to create a separate file in the book's directory and never ever update the actual eBook if customising.
Otherwise the book is carrying that info if it's exported or copied to an eReader. After all the main points of Calibre are to organise for a physical reader and secondarily to cleanly convert formats.
Calibre may add a bookmark already? Certainly I export to disc before opening an ebook in the viewer if it's going to be uploaded as the viewer seems to add something to an ePub.
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