That's something really odd. This app was made using a very simple python code (less than 1000 lines) and no other user reported such issue. I really appreciate if you could attach some screenshots here or mail to: bukkbeek3d@gmail.com
I feel like this is some sort of shortcut infecting virus on your computer, because it has removed only the shortcut on your desktop (not the app). If you could look into the second notification (which is 7 hours ago) and if it's the same (infecting .lnk shortcuts), you should probably run a full system scan. I would advise you to run a deep scan right now, using bitdefender/ windows defender.