one of my customers was running his generator connected through a GE safety switch/ manual transfer switch when utility power came back on one arc fault breaker was damaged, two garage openers , one motion sensor switch and electronics on gas range ,He has used the transfer switch for three years with no problems ,I have the same one on my house and use it all the time in the winter and have had no problems , somehow a surge had to have come through the neutral as the hots are completely disconnected from utility when in generator position how would this happen and would it be wise to put in a separate knife switch in to disconnect neutral from the utility when gen is running.
Installing a separate knife switch to disconnect the neutral would not only violate the NEC but also cause the exact damage you have described!!!
My first thought before I read all the way thought the post was that you had a 4 pole transfer switch that also transfered the neutral, I have had in one case where the neutral pole didn't make contact when the transfer switch returned to utility, the results were kind of what you described, one reason I don't like transferring the neutral, and avoid doing so.
the damage you described sounds like a lost neutral, when it happened is the question, may I ask what was the reason of the power failure?
If not known, I would be in contact with the POCO or the line men that works this area and at first don't let on as to why your asking to see if they give you a clue to why this happened, like a car hitting a pole near by, or a connection failure at this transformer?