I don't know if I understand, but I'll try to give my idea even if it's not exactly what you want.
Instead of directly manipulating the objects in the scene, I would make different arrays for each object. For example:
An Array for chickens, where the number of lines would be the number of chickens. With each new chicken, a new line is created.
In the columns, you can put its X position, Y position, and if they have more than one color, another column for the Frame of each one.
The same idea would follow for the other objects.
This way, when you read the time, you just need to read the arrays to know the position of all the objects at the same moment. And create them according to the scene that is currently loaded.
When time passes, you manipulate all arrays so that the change is synchronized between all of them.
Sorry if that's not what you want, that's just what I understood from your problem.