These two games have two entirely different family save files (VirtualFamilies1.ldw and VirtualFamilies2.ldw). As long as you do not play the family that's sleeping, you won't open their family save file and they are not disturbed. If you open the other family that is supposed to be sleeping, you will most likely find they are exhausted since they were sleeping or in their sleep cycle and you woke them up. In short, one family does not know about the other family, they have two different family save files and playing one family will not affect the other family.
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WARNING: I cannot be held responsible for the above as apparently my cat has learned how to type.