As a contractor, I think it's very important to provide new, good looking materials to my client. When buying Sheetrock the other day, I rejected several sheets that where perfectly fine, but had some ugly coloring to them. My client doesn't know this, but in my opinion, hanging those ugly sheets would have looked bad until I had them painted. I feel the same about the trusses in the mud. I have no idea if they are damaged it not, but since the using of them is of some concern, the right thing to do is replace them with new ones that look new. It's what he paid for!!!! I also don't believe in trying to talk a client into ugly materials. Its counter productive to the overall job, and good referrals in the future. It's their money, I give them what they want.
I don't think simply replacing all of them is right or necessary or what I have asked for. They are going to come out and inspect. I suspect some will have to be repaired in the field and some will have to be replaced. With engineer stamped papers for the repairs I am comfortable.
As for them being just dirty I am not sure that I care if it does not effect the functionality.