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An empty collection is a perfectly valid thing on the device. And you can delete it through the interface. Find it in the Collections list, long press on the collection and select delete option from the menu. This will also delete the tile from the home screen.
If you are doing the collection management from calibre, you need to select the option to delete empty collections in the configuration. Otherwise, calibre will leave them there. And when calibre deletes the collection, it also deletes the row from the Activity table to remove the tile from the home screen.
And if a tile on the home screen ever gets disconnected from what it is supposed to show, long press on the tile and select "Dismiss tile" to remove it.
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