The real failure here is that you shouldn't be able to move the drive links out of the drive folder, since semantically that does not actually move the files.
(Filed a bug, but I'm not on the Drive team so I can't really take responsibility for this getting fixed. It does seem like a problem to me, but I don't know their infrastructure nor the limitations of shell extensions, so I can't really comment on whether a fix is feasible either.)
Or stop trying to force a connection between Google Drive's file view and Google Docs.
Move the links out of GDrive all you want, it should have no effect whatsoever on the hosted GDocs. They're just links, after all. Since when does moving or deleting a link delete actual data?
Someone at Google tried to force a connection that doesn't even make sense, and this is the result. Whoever decided that moving a link out of a folder should delete the hosted document should be fired.