No just the navigation. IE: Destination and menu no longer work but all other controls work Options, climate and audio still work on the screen.

 

I made the same mistake. 04 GX470 with Gen 3 NAV.

 

Got this from the internet for 2005 LS430.
Not sure if it works!

Preparation
1. Set the hand brake, remove the key from the ignition switch, and open the hood.

2. Disconnect the negative battery lead from the battery terminal using the adjustable wrench. This will prevent any possibility of shock or shorting during the project.

3. Remove everything from the trunk including any protective mats lining the bottom of the trunk and leave the trunk open.

Resetting the Navigation System
1. Lift up the panel in the trunk that covers your spare tire.

2. Locate a square metallic box on the right side of the trunk. Use the screwdriver to remove the two screws holding the box in place.

3. Unplug the all of the wires connected to the box. Remembering where each wire is connected to the box is unimportant. Each of the wires is designed to plug into only one slot. Remove the box from the back of the car once all the wires are disconnected.

4. Unscrew the eight screws that hold the boxes rear panel in place to reveal two electronics boards.

5. Disconnect the left electronics board and flip it over so you can see where the two ribbon cables connect.

6. Disengage the two brown colored clamps that hold the ribbon wire in place on either side of the electronics board using your fingers. Disconnect the ribbon wires. Let the apparatus sit disconnected for one minute while the the computer resets.

7. Reassemble the navigation system following the steps given in reverse order.

8. Turn on the vehicle and test to make sure the system is working properly. Follow the directions on the screen.

 

Something so DUMB check and make sure Keyless entry has all doors locked or unlocked as expected

 

 

 

 

I'd try another dealer. Can't believe they just say they don't know anything.