Originally Posted by chaley
Calibre has no role in this scenario. When you delete a book using the reader, the reader also cleans the collections. Calibre does notice that the book went away, but nothing further is done regardless of the setting of the option.
I too wondered about this question.
The slight confusion comes from the fact that the collection doesn't don't go away as soon as you delete the last book.
It doesn't go away until you connect then disconnect from the computer. Most folks do this when using calibre so it looks as if calibre cleaned the collection off of our device for us. Since you said this is not the case the collection must disappear on disconnect when the Sony device looks to determine what books/collections still exist.