Sorry to hear mate .. very odd behaviour.
On a positive note - there is no single code for a car key fob, that can be stolen. They are rolling codes, which means they are constantly changing. This means that if they want to break into/steal the car again they will need to do the same as they have just done.
What normally happens in these situations is they gain access to the vehicle either by physical IE smashing a window or using a repeater. They then connect to the OBD port and program a new key so the rolling codes don't make any difference.