Bewildering Smart Key Issue...new.

So I'm new here, but not new to troubleshooting and I've got a new problem that I can't find in the forums already. Had major work done to 2009 Prius, repairing mainly accident damage to the undercarriage ($7200!). Regardless, I got the car back and now the keyless start is not working. I can open the doors with the remote both automatic (proximity), and with the key fob buttons and the panic button works too. I have replaced the battery in the key fob, I've now got even better range to unlock it! But I still had the same issue. When I get in to start the car I have to insert the key for it to start. It will not start without the key in, it gives me the "orange exclamation with the key" light and won't start without the key in. The 12v battery is great, heck I jump started my 92 F250 with it just the other day. Also tried the "key" button under the steering wheel. Didn't do anything except make the warning light STOP coming on.

So I've tried all the usual tricks and still don't get to use the key in the pocket/purse like I did before the car went into the shop. My question then is is there a reset/recognition procedure that I can try? I only have the one fob, the one with the silver logo. I don't know why resetting this would make a difference, since I can unlock the doors I would think something in the car IS recognizing the key, but hey help me out. I'm going to have to return the car for further repairs and I'll put this on the list of things they need to take care of if I can't get a quick fix here. I wonder if having the battery disconnected for so long (it was in the shop for almost 3 weeks) reset something? do not know...Please help!