LOL I have the exact reverse of this issue.... on my last Kindle Paperwhite Next Gen the shadow of the book remained in my collection and I liked it that way because it made it easy to see what I had read and what was in storage for each collection. On the replacement Next Gen I lost that feature
My cunning plan was to dump my full library into personal documents and sort them into collections and then remove the unnecessary files from the device. My thinking was that this would make finding all the necessary files for any collection much easier if all you had available was a kindle, a wifi hotspot and a poor memory lol