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I have noticed something similar.
When I add books to my kindle, I also make a new version of the catalog I keep on the device. With the new database, the new version of the catalog shows up as a new entry in the book list in calibre.
Both entries in the list points to the same files in the library-folder. And removing the catalogue from the device, removes the Ondevice-tick from both entries.
The duplicate entry disappears with a restart of calibre.
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