i think it falls under the 5 year 60,000 miles part. They replaced mine on my 2011 santa fe last year for free mine went for a swim in the pool.. They were good about it.
When both stop working there is an issue with the RKE system, not the fobs and the dealer should cover that if you are still under the basic bumper-bumper warranty. Reprogramming is not the answer as they just don't "loose programming" even after a power disconnect.