Have you tried resetting the one touch window control? When you disconnect your battery the car forgets where the top and bottom of the windows are so you need to tell it.
Wind the window all the way down holding the button on the door. Hold it for a couple of seconds then wind it back up until it closes. Again hold it for a couple of seconds. Now your window will go down and up with one touch from the door controls. I assume that this will then also reset the keyfob to be able to open and close remotely.
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