Edit in JSFiddle

var ids = 1;

var myParentClass = (function(){

    var _protected_prop = {};

    return new Class({

        initialize: function(id, par1, par2) {
            
            this.id = id;
            
            _protected_prop[this.id] = {};
            
            _protected_prop[this.id].prop1 = 'myvalue1';
            _protected_prop[this.id].prop2 = true;
            _protected_prop[this.id].prop3 = 65;

        },
        protectedProp: function() {
            return _protected_prop[this.id];
        }.protect(),
        changeProp: function(value) {
            _protected_prop[this.id].prop1 = value; 
        }        

    });

}());

var myChildClass = (function() {

    var _protected_prop = {};

    return new Class({

        Extends: myParentClass,
        initialize: function(par1, par2, par3) {
            var id = ids++;
            this.parent(id, par1, par2);
            // here the protected prop of the parent are ready
            _protected_prop[this.id] = {
                prop4: 'myvalue4',
                prop2: false
            };

            _protected_prop[this.id] = Object.merge(this.protectedProp(), _protected_prop[this.id]);
    
        },
        test: function() {
            $('test_result').appendText(_protected_prop[this.id].prop1 + ' ');                    
        }

    });

}());

var c = new myChildClass(1, 2, 3);
c.test();
c.changeProp('myalteredvalue');
c.test();

<div id="test_result">risultati: 
</div>