If you over-discharged your LiPo, the conducting material inside the cells will start dissolving into the electrolyte, it will also start plating electrodes causing internal shorts within the battery. If you try charging such battery you may initiate thermal runaway. Once shorts happen, damage inside at first unnoticeable will continue, battery will puff quicker, it will have higher internal resistance and will continue building up shorts and getting more dangerous every use. Just dispose such a battery, especially that you had it discharged for longer, it's not safe.
I suggest you set your charger into discharge mode, then once discharged return it to the nearest battery/explosives/unsafe materials storage place.