I might be wrong (again), but it sounds like the shortcut removal tool identified a few shortcuts that haven't been used and he gave the go ahead to remove them.
I did the same thing and when I tried to put them back on the desktop that utility prevented it some how. I had to remove the programs then re-install them to get the short-cut back on the desktop.
I will never use that thing again as it does cause you a world of grief.
Buttonpusher69