Interesting diagonosis

I'm sorry to hear the bad news. Is there anything that you can do to get the exact codes? Most of them are P0Axx. Just get the codes and otherwise ignore the person behind the counter. It is rare that a service advisor knows anything about a Prius, other than it is easy to scare people.

autobeyours.com in Scottsburg, IN, is a ways away, but it would be your best bet for a salvage inverter, battery or transaxle, if that turns out to be the problem. Better that than a $4,000 repair at a dealer that you don't trust.

Did you open the hood and check to see if there was turbulence in the inverter coolant reservoir when the car is in Ready, as shown in the video?

 

It still sounds like they botched installing the water pump. What will happen with a bad pump is that the car will operate normally until the inverter overheats. When that happens, the warning lights come on, but the car will continue to operate. But with the inverter no longer charging the 12V battery, it's going to drain rather rapidly. Eventually the 12V battery will reach a level of maybe 10V and the electronics goes wonky.

The first ECU to fail because of low voltage varies. Some units can just tolerate out of spec voltage better than others. But even at low voltage, an ECU may retain enough functionality to declare itself sick, and set the a DTC. Or it may just make incorrect decisions, leading to failures in other parts of the system.

So eventually you're at the side of the road and turn the car off. If the smart key system has failed, then it may block the normal method of turning off. Plugging the keyfob into the dash uses alternate equipment that may still be operating.

Once you've stopped the drain on the 12V battery, it recovers slightly over the next few minutes. If you turned the car off at 10V, the battery may recover to 10.2V. If you wait long enough, the inverter may even come back to life. So you can start the car again and it will work until the 12V battery goes too low again.

Eventually the car gets to the shop, and they try to pull the codes. The list will consist of all the ECUs that couldn't tolerate the low battery voltage. Mind you those same ECUs work fine when the voltage is normal.

The 12V battery will be flat. If it's on its last legs, it may even be identified as the source of the problems. But if recharging the 12V battery is successful, then it's not the original problem, only the victim.

Hopefully the inverter protected itself from permanent damage by shutting down. Once it gets normal cooling, it should work fine.

The most likely problem is that there is air trapped in the cooling circuit.

 

Yes, air in the coolant is all too common. Have them re-do it.

But please check the 12V battery yourself using the E-Z procedure given below. At that age if it was drained once it's almost certainly near death no matter what the dealer's pass-fail tester says.
http://priuschat.com/forums/newbie-forum/73400-weird-stuff-happening-mpgs-dropping-test-battery.html

 

I seems to me that the simple job of checking for flow in the coolant loop (by casual inspection of the turbulence/flow in the reservoir above the inverter) is something that all we all should take the time to do these days. I know that when I first heard of these types of problem that was the first thing I did, to familiarize myself with what it should look like when working correctly. That should give me a good reference point to compare against if at some point in the future I ever have this type of problem.

This procedure is as easy as checking the dipstick and I think it's something we all can do. It's really annoying to hear so many tales of the dealers stuffing up this simple issue. My condolences to the OP.