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That is not OEM installed...........they never put things like that on the roof. You repair soft spots on the roof from the outside. The trim has to be removed so you can get the rubber membrane loose and pulled back. It sometimes requires cutting it and repairing that later. I think this would be better answered over the phone with some communication on what and how to proceed. A photo of the damaged are would help if you can attach one to your post. All follow ups are included in our fee. I repair lots of these in my shop.
Just checking back in to see if you were able to resolve this or do you still need some additional input from me here?