I have just experienced my first run-in with these ghost parts. I poked around on a lot of websites and found a few fixes. The only thing that worked for me though, was to add two options to the config.pro file. The options are cleanup_drawing_dependencies and cleanup_layout_dependencies both should be set to yes. I had to open both the layout and the drawing, regenerate, and save both files. I could then delete the ghost objects from my workspace and they haven't come back yet. Shoot, I better find some wood to knock on! Good luck.