To change a break points list for the given path element, use the method com.nomagic.magicdraw.openapi.uml.PresentationElementsManager.changePathBreakPoints(PathElement, java.util.List). The same method must be used if you want to change a client or supplier connection point.
The following code snippet shows how to do this:
    PathElement element = ...;
    ArrayList points = new ArrayList(); 
    points.add(new Point(100, 100));
    points.add(new Point(100, 150));
    SessionManager.getInstance().createSession("Test");
    PresentationElementsManager.getInstance().changePathBreakPoints(element, points);
    SessionManager.getInstance().closeSession();