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Calibre Metadata is like the old fashioned card catalog sitting in the middle of a Library.
Cards. Books on shelves. no physical connection. They just sit there.
In Calibre, if you want to update a book (create a temporary connection), You need to force that to happen:
Conversion,
Polish,
Modify EPUB (a PI)
Any of these make changes to the books file IN the Library
Send to device/Save to folder update the copy (but not the one IN the Library)
Your other question:
USE filename ...
Only applies to ADD Books. This setting affects how the INITIAL book record (Library metadata) is populated. It does NOT affect the book in any way.
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