Take a deep breath and think about the resolution. If they take up the durarok and pull all the nails (1 1/4" ones) are you confident that nothing has damaged or compromised the pex. It is very forgiving, however you don't want to have to deal with a repair later. If you think that after all the nails come out, and that no penetration has occurred, you could once again re rock it, glue and screw it down and sleep peacefully. A total removal is a much bigger issue, and you will have to see how that works out for yourself. If you have a cats paw or a wonder bar, try removing the roofers yourself. If they come right out, you will be happy knowing that. I know this is about making it right, and that is why I have lost lots of sleep in the last 40 years in this business. Doesn't matter if it is dirtwork, concrete, framing, electrical, plumbing, insulation, heat/ac....or a durarok mistake; you can fix it and not die or become disabled because of it.
Looks like you may miss the big snowstorm out where you are. Nasty mess upcoming for the NE..all the way back to Alabama!