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Normally, the calibre database and the metadata.opf are where the changes are stored and the library copy of the ebook is not modified. You will need to use either Save to disk or Send to device for calibre to update the metadata in the sent version of the file. To modify the metadata in the calibre library copy, you need to save the metadata to the ebook file. I use either Polish (AZW3 and epub) or ModifyEpub (epub only).
Personally, I would not recommend dragging and dropping files directly from the calibre library. Too much of a chance of an error toasting part of your library. So save the books to disk and then copy from there to your iPad.
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