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Yep. Bzzzt.
That is not how Kobo or many others work.
You (caused a) changed the file name (as affected by the Save... template), so the Kobo treats it as a New Book.
Kobo stores the Metadata during /Processing/ after you eject. That is where Calibre is doing the match
There is no simple work around If you change anything the save... template uses. Title and Authors are mostly mandatory (the resulting filename MUST be unique or it will stomp the previous file)
To update any other metadata on the device: use the Update metadata choice in Kobo Utilities Plugin (there is also an item for when the TOC gets affected)
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