I believe there should be a config option "cleanup_drawing_dependencies"set to"YES". This will then give you a warning, but if you delete as it says to, it should take care of the problem. I still see these warnings occasionally on drawings that were done pre-Intralink and have not actually been open in Intralink thus far
We experienced this allot since we use the Merge and Cutout functions for just about all our designs. When we don't keep the assembly that was used to create the Merge or Cutout on the model. We see Ghost Object Issues.
We looked at using Inheritance as a better option but the flexibility with Inheritance features is too risky for what we are trying to control with Merge and Cutout features.
"Too many people walk around like Clark Kent, because they don't realize they can Fly like Superman"