To reflash the Lego firmware please follow the following steps:

1. Connect the device using the USB cable. You can verify the connection
by checking the /var/log/messages file for the message similar to the
following:

kernel: usb 5-1: new full speed USB device using uhci_hcd and address 13
kernel: usb 5-1: New USB device found, idVendor=0694, idProduct=0002
kernel: usb 5-1: New USB device strings: Mfr=0, Product=0, SerialNumber=1
kernel: usb 5-1: SerialNumber: 00xxxxxxxxxx

where xxxxxxxxxx is a device serial number.

2, Press and hold for at least 5 seconds the reset button hidden in the
pin hole under the USB port. You can check whether the device entered
reflash mode (a.k.a. SAMBA mode) by checking the /var/log/messages file for
the message similar to the following:

kernel: usb 5-1: new full speed USB device using uhci_hcd and address 10
kernel: usb 5-1: New USB device found, idVendor=03eb, idProduct=6124
kernel: usb 5-1: New USB device strings: Mfr=0, Product=0, SerialNumber=0

The device should also produce clicks in the speaker (about once per second).

3. Flash the firmware using the following command:

    su -c 'nxt-fwflash firmware-image'

where the firmware-image is the firmware file.

While flashing the output should be as following:
Checking firmware... OK.
NXT device in reset mode located and opened.
Starting firmware flash procedure now...
Firmware flash complete.
New firmware started!


Official images can be found at the following URL:
http://mindstorms.lego.com/en-us/support/files/default.aspx#Firmware