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I have read that the power windows need to be reset after a battery change, but never the key fobs. The small battery in the fob itself is recharged while inserted in the dash. I wonder if that fob battery is dead, rather than a programming issue.
I just replaced a totally dead battery--so dead, not even the dome light went on, and the AAA guy could not get the thing they use to check batteries to register any power at all. New battery, and everything worked as it should.