I see what the real question is now :P
What you need to do is run the simulation of time passing when you enter each layout/scene.
To do that the first thing is keep track of the time when you leave a scene so you can calculate the time difference when you enter it again later.
If you know the last time you where in a given scene and the current time, you can tell how much time has passed.
Assuming everything is in the same place and has the same state as before you left the scene, you need to be able to tell each object in the scene to do all the things it would have done in the time that passed.
Taking from your example, if you left a scene at 30 seconds after the game started, and came back to it 60 seconds after the game started, that means that you need to figure out all the things that would have happened in those 30 seconds, and make those changes.
For instance, and to keep things simple. If a hen were to reproduce every 5 seconds, in 30 seconds there would be 6 (30 / 5) more hens that spawned from the original hen. If the original hen should move randomly every 2 seconds, it would have moved a total of 15 (30 / 2) times.
That only takes care of the first hen. The simulation should also take into account what happens to the new objects that would have appeared during the elapsed time and what would have happened to them.
All of this is easier said than done. I suggest you start real small and then build from that.