Gonna bet the easiest and most likely thing is they will come back and say you need a new ECU. Should solve the problems and a lot less diagnosing for them to do.
Well I just got off the phone with him and he said he couldn't find any blown fuses. But said that he doesn't think the ecu is gone just missing files but he is going to pull it out today and look at it some more
It's also worth mentioning that you are not meant to put the earth jumper cable direct to the battery when trying to jump start the MK6! I wouldn't be surprised if you actually have an immobiliser issue!
Well alright here's the update. Over the past week he has replaced chips and resistors thinking he could save it but today he called me and it's not even worth trying to save anymore and that he found one in Florida which he ordered. Car will hopefully be up and going by Friday if not it will be Monday or Tuesday