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That is the normal function of calibre: Don't touch the Original IN THE LIBRARY.
Using Send To... Save to... update the copy being sent , on the fly.
There are ways to force the metadata update, you just need to add them to the toolbar: Polish or Embed metadata.
Then there is Modify EPUB plugin.
Each has its (DIS)advantages, so review the manual or PI description in the dedicated thread here at MR
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