Assume that the batteries are exactly the same except for that one has been partially discharged.
From my understanding there is very little charge stored at the terminals of a battery, but rather charge is generated from the chemical reaction when a circuit for the battery is completed, meaning that the positive and negative terminals are connected. So when you attach the batteries in parallel, neg to neg and pos to pos you are not completing the circuit, but somehow the voltages equalize between the two meaning that current has to flow. So how does the current flow between them if there is very little current stored at the terminals and you are not really making a circuit?