I too had a main bettery replaced at 163,000 miles. To my surprise they said the replacement battery warranty is only good for 12000 miles or one year. Cost was $1800 plus a new ecu - $600 something. That seems to me like an awfully short warranty for such an expensive part. I did call
Toyota in Calif. They said that the warranty on the replaced battery is 12 months, but unlimited mileage. Stinks, to me.
Anyway, after going some 35000 miles, I got the main battery warning light again - too late for the warranty, which had expired. I had read somewhere that the main battery warning light would go off if you disconnected the auxilliary battery, which I did. When I hooked it back up, the warning light went off. I have this happen three times recently, and after disconnecting and reconnecting the aux. battery, everythiing works fine - no warning light.