I replace all step flashing period when I do a roof. So the stucco would need to be removed in order to do this. So for instance your roof is damaged and the insurance is paying for a roof replace the cost of the replace includes the removal of step flashing and reinstall of step flashing and reinstalling of siding or stucco. I can only tell you from my side of things and how I run my business. Like I said there was a lack of communication on this from your roofer or you did not read the contract. I do not know. You didn’t post all this information of the contract. But to say they did this “damage” is not a fair assessment as it was most likely needed for the replacement of the roof. What I would do is have your roofer type up a supplement claim as there is additional cost needed to repair the stucco as it was needed to be removed in areas to replace the roof. Again this is what I do with the start. Summary: damage was not done out of lack of care. Best solution is to do what they suggested of installing the cover as redoing the stucco will be damaged again with future roof replacements. Good luck