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You can also inject the current metadata into the library copies of EPUBs (and AZW3s) with the Polish Books tool. There's also an Embed Metadata tool.
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For years my workflow has been add book, fix metadata, Polish. For some small change if I spot a rock, like changing a tag, immediately hit Embed Metadata. Doing this, I've never had a problem with what is actually in the book compared to what I see on the Calibre screen.
(I keep Polish set to update the metadata, and also update the cover, smarten punctuation, and remove unused css rules. Keeps everything nice and clean.)
This seems to keep coming up over and over again...maybe a sticky about how Calibre handles metadata, and Polishing?