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Window Indexing and Express-Up Reset
Window indexing may be required if the vehicle battery has been recharged or disconnected, or is not working. Express-up and the convertible top will not function until the windows are reset. After battery power is restored, a message or code displays in the Driver Information Center. See Driver Information Center (DIC) on page 5-23.
Once power is restored:
1. Close the doors.
2. Start the vehicle.
3. Put windows down
4. Raise each window and hold the window switch up in the fully closed position for a few seconds after the window is up.
If that doesn't fix it, then check the battery connections. Some people who were fairly handy with tools still had problems with the connections after battery replacement.