I had my spare set of keys stolen from my house. What are my options?

Please shoot holes in my plan: I plan to get a new key blank and a new FOB. Dealer will cut/program the set. However... the stolen set is still out there. I understand that the dealer can clear the fob, but can the dealer clear the stolen transponder key code?

I can live with the stolen key matching the cylinders in the door/ignition, but if the stolen transponder key can be cleared, it wont start the vehicle - right?