If you cannot account for one set of keys and worried that it could fall into hands of someone that could steal the car later, I  would think you could go into immobilizer function menu and see if there is something in menu to erase all the keys and reprogram your remaining keys, but do it in the dealership service parking lot, to save yourself a tow  in case you cannot reprogram your keys.

 According to the Function Viewer, you have immobilizer programming for SantaFe`s from 2006 and up.

 You have to have the Pin and the dealer won't give them up :-(