I do have the same issue.
If I set a series on Calibre then send the book to my Kobo, the series shows on the Kobo.
However, if I send a book without a series, but then after set a series in Calibre, I can not synchronize the series with the Kobo.
I tried the 'update metadata in device library' and the 'update cached metadata on device' without success.
The only way that I can make it work is to delete the book from the Kobo and send it again.
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