Car stolen (but recovered). Key cloned and extra key registe

[Queeve2000]

Hi all, my Rav4 was stolen recently but recovered. The key was cloned and a new key added to the car. I've been into my local dealership and no one seems 100% sure how to reset the keys and/or remove the extra key.  One person told me I needed new keys, then when I took it in I've been told I need a new transponder as that's the only way the key code can be changed.  Any advice gratefully received. 

[ToyotaGSL]

How was the key cloned?

(don’t know the answer to your specific query).