Error Code P0607 upon picking 2013 prius v up from muffler shop after stolen cat converter repair

My catalytic converter was stolen in February and had been sitting at the muffler shop until the day before yesterday. The thief cut the wires for the O2 sensor so that was replaced during the repair. When I picked the car up the check engine light was on and the drive felt very slightly rougher than usual, neither of which was the case before the cat converter was stolen. Muffler guy told me to take it to the dealership for diagnostic and there was a language barrier so somehow I thought there was something only the dealer could deal with, now I realize I can probably just take it to Autozone for the followup diagnostic (maybe?)

I took it to the dealership and they said I need to drive it around for 3-4 hours total before they can run the diagnostic. Here are the notes they gave me verbatim:

Intake: "Customer states their vehicle was at a muffler shop since February waiting on a catalytic converter, just got the car back and now there is a check engine light. Thinks it may be related to when they stole their catalytic converter."

Mechanic: "Vehicle needs to be driven more, customer will return after driving it for a day or so. Need more diag time to confirm if parts need to be replaced. Vehicle has code P0607, P2196, and P0138. P0607 is for control module performance and will need to test drive and complete monitors for P0138 and P2196 to determine if ECU needs to be replaced or AF and O2 sensors need to be replaced."

From my basic research it sounds possible that I need an ECU replacement since the drive is a little rougher than before.

Could any of this have been caused by the sheer fact that the car was sitting undriven for 5 months? I know for a fact that there was no check engine light on before the cat converter was stolen and insurance obviously wants documentation to prove that this issue was related to the theft before they even consider paying anything. In my mind the car sitting there forever is directly because of the theft but that probably won't fly.