To verify I have the scenario described accurately, you have a persistable class with a default value for a field IntArray, defined as an array with 50 elements. You have played the map where this definition exists, and as part of playing in this map, an instance of this class is constructed and inserted into a persistent weak_map. The map has been updated such that the default value is now an array with 100 elements. Upon playing the map, your entry in the persistent weak_map still only has 50 values.
If I have the above accurate stated, I believe this is expected behavior. The default value of the class is only used at the moment the class is constructed - effectively, the instance is constructed with fields copied from the default values, but then there is no longer a reference by the instance to the default value. Such an instance is saved (with just 50 elements in the array) when you originally played the map. Changing the default value will have no impact on that instance.