The script that you delete is connect to another script or a button on your layout. You will have to update the item to your new script. If it automatically popup on the screen when you open the layout then I would look at a script trigger on your layout.
One script can use the Perform Script script step to perform another script. If you can identify the script being performed when this message appears, open it in the script editor and check for a Perform Script script step that attempts to perform a script that no longer exists.