Add logic to only delete desktop icon if there is not a icon already there.
I originally was using the feature to delete desktop icons after updating apps with Intune. The problem this caused was that there were several people who already had icons on their desktop and liked them there that had their icons deleted. So I turned off this feature but this caused the issue of those who keep a clean desktop being annoyed that new icons keep showing up on their desktop. I propose adding additional logic to your script runner to detect if the application already has an icon on the desktop. If there is already an icon there, don't delete. If there is not an icon there before the update, then delete any new icon.