Our contract plainly states that rotten decking found will be replaced at $xx per sheet. We also use what we call a pre job check list we go over with the HO that sets expectations and again covers the fact rotten decking will be replaced and charged for. In order for the roof crew to get paid for rotten decking, they know they have to take pictures and send to me. If questioned by the Customer when we present the invoice, we remind them of the contract, the pre job check list and show them the pictures. We rarely experience any problems getting paid for rotten decking.
Often, not always, you can detect a potential decking problem when inspecting the roof. That generally leads to an inspection of the attic to see if we can detect anything from that side. Either way, we alert the HO to the potential problem AGAIN setting expectations appropriate up front rather than popping a surprise on them when we're done.
The vast majority of the time it's all about properly setting expectations.