If I remember correctly, if the battery dies or is disconnected on 7th gen Accords, it looses auto window function. The windows will still roll up and down with normal power window control, but the auto function is disabled. To reset it, I think you have to shut the car off, hold the driver's window switch up, and while holding it turn the ignition to run. Continue holding it untill you hear a beep or a series of beeps, and it should be reset.

I don't know if I am 100% accurate on the steps of this procedure, so you may need to contact your dealership's service department. But I do know there is a procedure like this which must be performed to reset the auto up/down function.