Find out which VI's are calling that .ctl by right clicking and use Find Callers. Those VI's should show up as broken when you open them because they are going to look for the .clt file that no longer exists. Remove whatever is using that .ctl within those broken VI's until they are no longer broken.
Keep in mind that the controls maybe called in a disabled case of a disabled diagram structure as a constant. Then you would have the dependency, but the VI would not be broken.