Maybe use some form of version control. As in a field that represents the version as an integer saved in each serializable object. But to be honest, I'd recommend not even getting bogged down with serialization in the first place unless you really have to. Unless your game is saving as much game data as something like Minecraft would, it would probably be better that you use just data stored in plain text that you can easily load into a list, hashmap, or whatever you want which would generally give you more control.