Checkpointing does require a lot of resources and very large scale simulation like a simulation of whole universe may prohibit such checkpointing.

That depends on the scales involved in the universe where the simulation is being run. Maybe we're easy :-P

I cant help but picture two mice trying to reconstruct the question from a human brain

I was thinking of this one as I wrote that:

There is a theory which states that if ever anyone discovers exactly what the Universe is for and why it is here, it will instantly disappear and be replaced by something even more bizarre and inexplicable.

There is another theory which states that this has already happened.