What could be a potential cause of the Desktop icons and Taskbar getting lost while executing the workflow?
The Taskbar and Desktop icons are a part of the "Explorer.exe" process. If there is any impact to this "Explorer.exe" process during the workflow, by means of either a "Close Application" or "Kill Process" activity, this will shut down the "Explorer.exe" process and in turn result in the Taskbar and Desktop icons being missed.
One of the potential reasons of including a Close application/Kill process activity to close of the "Explorer.exe" process is to have it close down an existing Windows Explorer window. In this scenario, closing or killing the "Explorer.exe" is not a safe approach to close the existing Windows Explorer windows. The safest option would be to close off the Windows explorer window by using a Click Activity to interact with the "Close" button of the same window, or by passing an "Alt+F4" hotkey to the particular window.