Thank you for writing.
The message should indeed be just a warning and not an error. I tried reproducing the issue (deleting a bunch of shortcuts and then uninstalling or upgrading) but could not. Looking through our error report database I did not see any error report sent under your account.
Could you share an installation log? That way we can inspect that and possibly improve our installation experience and/or give you a better explanation for what happened.
I appreciate the concern for our processes and we are as always doing our best to provide the best products and services.
the Telerik team