I have been having the same problem. I placed a Word document into ID4 two years ago and have changed it considerably since. Every time I open the document (and also in the pre-flight check) it shows as a missing link. I started to Relink, but then it seemed to be replacing the new material with the old - not what I want.
It's only a little thing but having it show up all the time is a nuisance. Has anyone worked out a solution? There is no mention of "Unlink" anywhere, and I tried MattKelly's fix but "Update links" was greyed out.
ID 6.0.4, iMac 10.5.8
