Be careful you can only have 2 FOB's programmed, if you get a replacement FOB then it will replace one of the existing FOB's already programmed be safe take the other FOB with to the dealer when they reprogram to make sure it still works. Yes they do charge allot to do the programming.
Not sure if this works for all Santa Fe's, but if not, I'd search hi/lo for a means to purchase and program the FOB(s) myself. Absolutely ridiculous to pay anyone $50-100 for just programming. I've owned at least 6-8 FOB equipped vehicles now, import and domestic. None needed a trip to the dealer for programming.
The set switch was eradicated from the Santa Fe in the mid-2004 model year. Trust me, I know....I used to have one and when they had to re-program the remotes, I watched them do it with a plug-in computer. Why make it easy when you can make it hard and get some more money out of the customer?