Nobody has replied to this in a couple of years but as a customer that this happened to, I will tell you that the roofing company that I hired to replace my roof is taking care of the issue at no charge to me. I went looking on the internet to see how frequently something like this occurs and came across this thread.
I created an account just to offer something to think about for all you roofers that disagree that the roofer should take care of fixing this. Since they started work, I’ve had three neighbors ask how it’s going because they feel it’s time for a new roof as well. I can honestly say that if they had even tried to charge to charge me for fixing this that I would have told all of my neighbors that asked that it’s been a pain and would not recommend the company doing the roofing.
Now technically I may be totally wrong in feeling this way but, it stands to reason that my expectation in hiring a roofer is to take care of the problem of me needing a new roof, not to fix that problem but leave me with the problem of now not having AC or heat until I get someone out to fix this because a nail hit my ac line. If I had been left with that problem of course it’s going to negatively effect my opinion of the whole process and therefore the company I contracted to do the work.
Remember you’re dealing with a home owner, not a home manufacturer. I am not well versed in the pitfalls of your business and anything you do to help me avoid them only helps you via word of mouth afterwards.