I'm using ADE 1.7.3 so I don't know if later versions work exactly the same way ...
When I download a book the .epub file is stored in "My Digital Editions/" and a record is added to "My Digital Editions/manifest.xml". When I delete a book the record is removed from manifest.xml but the .epub file remains.
So to see if an .epub file is from a deleted book, check if it is mentioned in manifest.xml. E.g. on Linux this command run from within "My Digital Editions/" will list all the .epub files that belong to deleted books:
Code:
for F in *.epub; do grep -q $F manifest.xml || echo $F; done