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When you connect the device, the shelf management is done on the books that are in the current library and are also on the device. For a book on the device that is not in the calibre library, nothing should change.
With what has happened, it make me think that you have connected the partners device while in your calibre library and that most of the books on the device are in your library. But, only a few of them have the values in the columns use for collections.
The fix should be simple: Connect the device while the her calibre library is active. That should do all the shelf management again.
But, before doing that, check the shelf configuration in the driver is correct. And that the columns being used in both libraries contains the shelves as expected. The driver configuration is common across all libraries. But, the custom columns used don't have to be in both libraries. If you have removed a column from the configuration, that might explain why it has happened.
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