You are right about there being a great chance of theories breaking down. Because without observing the phenomenon, it stays in a state superposition. And because of this, this is why scientists invented the uncertainty principle, because they are unable to be measured. The uncertainty principle is not taken into account in traditional physics theories, which is why they cannot be used in these cases.
See, this is the biggest point about all this, we cannot really know what we can not observe. We can predict, we can average, we can guess, we can create theories.... but until anyone observes it or tests them, the true nature or beginning or cause of the universe is unknown.