2004 Prius - water damage to communication wiring from faulty windshield?

Hello. Has anyone encountered this problem or heard of anything about it? I have a 2004 Prius CVT-E with 160,000 miles. It gave me the check engine lights and after I drove it for a mile, it ran out of power and wouldn't accelerate, though it kept starting. After towing it to the dealer, they said there was a "loss of communication with ECMs and RCM junction connector for J18 for communication line due to water damaged from windshield leaking and shorting connector and junction block." There was also water damage to the carpet and headliner assembly (it was raining that day). They said that the windshield must've been installed improperly at some point, but I don't remember ever having to replace the windshield.

So is it possible that they can tell that the windshield was different from the original, and has anyone heard of any problems with original windshields? Also, has anyone encountered any problems similar to this or any tips and suggestions would be appreciated.