If you have CA, the fobs DO NOT recharge in the car. You have to replace the battery. Its a CR-2032, I think?
If you don't have CA, then the battery is sealed in the fob and must be recharged in the car. That said, I would not leave a fob in the ignition. As soon as you start driving the car again, the fob will recharge in the ignition. If the fob will not open the car (battery dead), then use the emergency mechanical key stored in the fob to open the door.