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There is no synchronization, simply an on device indication. That indication is based on the following criteria:
A book in the library is said to match a book on the device when:
1) The internal calibre library uuid matches
or
2) The metadata (title/authors) matches
If you have multiple books with the same title/author, they might well match multiple times, this is fairly harmless, since calibre does not actually do anything with the on device status, other than display it. So you will simply get multiple books being marked as on the device.
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