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Yes, you can manually close the sunroof as long as everything is mechanically ok.
If you drop the overhead console down you'll find the sunroof motor mounted directly above there. On the drive gear end of the motor, in the center of the circular drive area you'll find a hex where you can insert an allen wrench or socket. As long as the motor, drive cables and sunroof guide mechanisms are mechanically ok then you can crank the sunroof open and closed using an allen wrench or socket.