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You don't upload the books twice. You just update metadate (Koboutilities can do it).
The Kobo ereader has to detect the added book when you send it. That only happens when you Eject.
Then when you reconnect the series or other metadata only in the reader's database rather than in a book can be updated by Calibre.
It can't be done AT ALL on modern Kindles, nor Collections.
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