You could write a deep clone Method, which copies every value of every property of your Object to a new one.
Note i extend Object.prototype to avoid type checking and for simplicities sake, this could be changed, if you feel unpleasent with it
Object.defineProperty(Object.prototype, "clone", {
    enumerable : false,
    value: function(deep) {
    deep |= 0;      
    var type = typeof this;
    if (type !== "object") {
        return this.valueOf();
    }
    var clone = {};
    if (0 === deep) {
        for (var prop in this) {
            clone[prop] = this[prop];
        }
    } else {
        for (var prop in this) {
            if ( typeof this[prop] !== "undefined" && this[prop] !== null)
                clone[prop] = ( typeof this[prop] !== "object" ? this[prop] : this[prop].clone(deep - 1));
            else
                clone[prop] = "";
        }
    }
    return clone;
  }
});
Object.defineProperty(Array.prototype, "clone", {
    enumerable : false,
    value:function(deep) {
    deep |= 0;
    var clone = [];
        if (0 === deep)
            clone = this.concat();
        else
            this.forEach(function(e) {
                if ( typeof e !== "undefined" && e !== null)
                    clone.push(( typeof e !== "object" ? e : e.clone(deep - 1)));
                else
                    clone.push("");
            });
    return clone;
  }
});
Example output and a Demo
var first = {
  var1:0,
  var2:0
  var3:0
};
var second = first.clone(Infinity);
first.var1++;
console.log (first.var1,second.var1,second); //1 , 0
To apply this to your code, you just have to clone the Object app.Defaults = app.Variables.clone()
The first argument is the level of deepness. If omitted, only the first level is cloned, which would be enough in this case.