It means that the XML contains more than one “script” object. The script object is where your customization code lives. In order to see what’s really going on, you’ll want to open that XML in an editor. If there are 2 of them - you’ll need to figure out which one is correct, that will be a little tougher.
I am unfamiliar with the auto deletion when multiples are detected…I wonder how it determines which to keep?