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This is not a problem at all, your Sequoia is very advanced with computers covering almost all functions including your windows. Whenever your battery is changed you will need to re-initialize the passenger window, to do so simply go over to your passenger door, make sure the ignition is turned on. Use the passenger door window switch to raise the window all the way and continue holding the switch in the up position for over 1 second, then hold the switch to lower the window and hold for over a second. Roll the window up all the way and you are done. The window will operate normally.
Did you get it working?