Did you re-initialize the indexing feature of the windows after reconnecting the battery?
If not;
Power Window Initialize
After a power reconnect such as battery replacement, the
window index-up feature will not function until the system
is initialized. Once power is restored, do the following:
1. Close the door.
2. Raise the window by pulling up the switch.
3. Hold the up switch for three seconds after the
window is closed. Release the switch.
4. Hold the up switch again for three seconds and
release.
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