[ BUILD # : Beta ]
[ JDK VERSION : 1.5.0_05 ]

I create a new class, called NewClass in the package newpackage.

I have that as main comment for the class.

/*
 * NewClass.java
 *
 * Created on 3 octobre 2005, 23:47
 *
 * To change this template, choose Tools | Template Manager
 * and open the template in the editor.
 */

I choose Refactor, Rename and be sure that Apply Rename on Comments is well selected, and click on Next.

In the Refactoring view, I can see that // * NewClass.java would be taken into account.
(see screenshot in attach)
I click on Do refactoring
Class is well renamed into MyClass. File is well renamed into MyClass.java. Comment of the constructor, and the constructor is up-to-date.
But not comment of the class.

Look at here:
/*
 * NewClass.java
 *
 * Created on 3 octobre 2005, 23:47
 *
 * To change this template, choose Tools | Template Manager
 * and open the template in the editor.
 */

package newpackage;

/**
 *
 * @author Vincent
 */
public class MyClass {
    
    /**
     * Creates a new instance of MyClass
     */
    public MyClass() {
    }
    
}