It looks like they screwed it up when they had it apart. What you have labeled as the fan wire is correct. It goes to the connector with the orange and black wires, which goes to the fan. All the slack is secured by the wire tie, but it shouldn't be pinched behind the plastic evaporator housing. Its a good bet that is your problem, if it didn't short out and take out the controller as well. At least now you have enough knowledge to hold them responsible it they messed up, instead of just paying big bucks for the repair.
Well, it's in the hands of the service center now. They moved my service up to something like Wednesday, which was a major conflict to my schedule... so then said to bring it today, and they'll give me a loaner, and work on it this week. (another challenge is charging an S with a 110 outlet, because the HPC for the roadster doesn't fit the S... only solution is lots of patience).
I attempted to demonstrate the fan to the tech, and it started blowing... How annoying. The tech laughed and said that's because the car knew it was in the service center. I also said it was really suspicious that I watched the "service due is xx days" count down, and the exact time it hit zero, is when the fan died. He said "amazing coincidence", because it is very unlikely that the annual service had anything to do with the failure.
I showed him my pics, the video, the noise, and the wire where it was pinched. He also agrees that the wire is pinched, but he also says there may be a dead spot on the fan that it moved off of when it vibrated during the drive in. So I will have to trust what they tell me on that one. Because I won't be there to see him open up the cover and inspect the harness. I did voice my suspicion rather loudly...
I do know a fellow owner who is on his third fan because previous ones all had dead spots. But for him, it was warranty, not something that happened after 6 years.
I'll let you know how it plays out. Thanks.