The RDM (rood door module) is very susceptible to stray voltage. When it gets damaged, the roof, windows, door locks, or all the above will fail to operate properly. Changing or jump starting the battery has been suspected of causing the RDM to fail. Here is a method to change/jump the battery to prevent possible damage to the RDM.
You might want to lower the windows slightly before removal because the window will not drop after fuse removal, and will get caught in the rubber seal causing the door to be hard to open. Remove fuse number 28 and 40 from the rear fuse block located the passenger seat on the water fall. Also remove the relay/breakers 01 and 02 at the top of the fuse panel. Removing these items will prevent current going to the RDM circuits until the battery is replaced.
ALSO, when jump starting, DO NOT connect anything to the main fuse panel terminals, use the red connection in the engine bay or the battery for positive, and use the alternator bracket bold marked ground or frame for a solid ground terminal.