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The setting is "Manual Management".
@Chaley: "If not set to automatic, then the series will be ordered using the indices when the book was sent, not what they are today in the database. "
I don't quite follow that sentence: the series I made where correct and not changed anymore, so on sending to the device from the database, they should be sorted as collections as stated by calibre in the preferences.
Quote:
"Manual management: Calibre updates the metadata and adds collections only when a book is sent. With this option, calibre will never remove a collection."
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