In which case the reprogramming has to be done by the dealer? For example when the car sat dead for months? Or in my case, when I swapped the Shift Lock Control ECU?

And only the Toyota/Lexus dealer can scan and reprogram it? Indies don't have such scanners?

 

If the car had dead batteries then you will need to leave the key in the ignition at the on position for about 6 minutes to resync.
http://www.lexusownersclub.co.uk/for...t-wont-go-out/

Unconfirmed but may require a master key.