>That means the master clips has indeed been deleted from the browser
Not in most cases. It usually means that the relationship between the clip and the browser has been corrupted. In this case, there is no workaround to it. Another scenario is that by dragging the clips from another project, final cut will not be able to establish a link to the master clip in the browser (as it doesn't exist in the browser of your project).
I just realized that when you do a copy and paste on your sequence (i usually make a duplicate), Final Cut actually forgets the link to the master clip on that sequence. I'm on FCP 5.1.4, is it replicable in FCP 6?