In my case, the Terminal Commands posted did not work...but this is how I got rid of the Duplicate Apps in my Parallels Toolbox Window...
I opened my "Trash Can", then I "Left Clicked" the Parallels Toolbox so that all of the Apps are showing and I Selected and Dragged the duplicate apps into the open Trash Can window, one by one...
As I did, the Duplicate Apps were no longer in the Parallels Toolbox window...
I then Emptied my Trash Can and restarted and powered down/up my iMac several times to make sure that the duplicate apps were in fact gone...as well as selecting each of the apps that had duplicates, just to make sure that they still worked...which they all did...
So, in my case, all is well now...
JFYI;
I am running Parallels Toolbox Version 2.0.2 (1213) and macOS High Sierra Version 10.13
Last edited: Oct 13, 2017