Recently on one my colleagues Lotus Notes whenever we went to "File > Preferences > User Preferences..." a dialog box used to show up saying "Document has been deleted".
After searching on Google I found this technote which indicated that if the user is assigned some policy and it has been deleted then this problem may occur and we had policies assigned to users. But technote is talking about problem on server. But still we decided to give it a try. And it worked!
- Open "names.nsf" on your local machine.
- Go to the hidden view "($Policies)".
- Press "SHIFT+F9" to rebuild current view (you must have Manager access on names.nsf). And you are done!