Good question! Yes, he could of taken the SIM card out of Melissa's phone if it was a GMS phone and put into a different GMS phone. He could of also "spoofed" the caller ID using Melissa's info with a phone of his choosing (GMS or CDMA).
But, IMO, he would of still had to taken additional steps to avoid being tracked besides just cutting the call at the the 3 minute mark.
What ever the case, it looks like he knew exactly what he was doing and how to cover his tracks. That adds a pretty disturbing element to the personality of this guy. The sister said he was in control. The step father said the conversation was more violent than sexual in nature. Lots of BTK type markers in my opinion. They need to catch this guy....