Dealership grossly misdiagnosed my car's malfunction?

I brought my newly purchased car(2013 Honda Accord) to my dealership due to mechanical and computer malfunctions. Basically, when I started the car one morning, all of the dash warning lights came on but the speedometer and tach were not reading anything. It was like the computer glitched and nothing was working correctly. The dealership said the malfunction was covered under my warranty and they would replace the dash lights and possibly the ECU to fix the problem at no cost to me. Great! They called me after a week of silence saying that neither of those were the culprit and they happened to "discover" chewed through wires from a rodent. Now they are saying the previous misdiagnosed repairs will not be covered and if I do not file an insurance claim I will have to pay $3300 for their misdiagnosis! How should I handle this? Is it too much to assume that checking those wires should have been first on their list? Now I have a new ECU that was not needed but they claim they cannot return it because it has already been programmed to the car. Help!

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