I had 2 screws come loose under the rubber on a roof once. But, I just cut a tiny hole, removed the screw, reinstalled with construction adhesive, then did the eternabond patches. No issues after that. I hope yours turns out great. To me, the more they mess with, the more possible issues I could have later. Got any pictures? At least post one of the new roof.
John and Rebecca Dickson
Emma-8 / Little John-5 / Iva-1+
2013 Ford F-350 Lariat FX4, CC LB PSD, DRW
2015 Jayco Jay Flight 28BHBE (#8)