I run down a lot of batteries when in the shop(performing test and such) although its not good for the batteryImages available only to Customers.
However if the battery is good it will charge itself back up during idle and normal driving. If I do run one down I will start the car and let it idle for a while. So to answer the question YES. The alternator senses the state of the battery charge the it will increase voltage to the alternator causing it to charge more on modern vehicles.
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