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Not sure if there is an answer to this - it depends on your requirements (and you might want both).
Saving the metadata in the opf file saves it in a separate opf file, but alwayws saves all the data and is fast.
Updating the metadata in saved copies is slower as it ahs to update files as it saves them, and may not be able to include all the metadata if the format being saved does not support it. However if you want the metadata to be recognised when you load the book onto a device for reading then it needs to be embedded in the file.
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