Do not try to reset them thru the EPDM - - you will damage the roof material. If you try to "reset" shinners, 50% of them will pull right back out. It is best to remove them and replace them with ring-shank nails with a touch of glue on them. Then, make the roof repair as Ratracer ably instructed you. And, as he stated, try to get the factory to take care of the repairs first. Good luck with that, but it is worth a try.
2003 Dodge HO 6 speed Laramie Dually, Jordan controller, RDS fuel tank, Air Ride 25K hitch
Carriage 36' fiver, Onan 6500, Prosine 2K inverter, 3 slides, MORyde IS and Kingpin