Agree with the others. If you have rot, you need to fix that. Pull the rubber back, fix the structure underneath first. Anything less is a bandaid on a bullethole. After that, Eternabond tape is your friend.
The peeling topcoat, no clue. Looks like its just a paint product on top of the existing roof. It offers no protection at all. Looks like your rig is a 1994 model. That roof is long past its expected service life. If you like the rig and the damage from rot isn't too severe, you should re-roof your entire camper. I wouldn't put EPDM rubber back on, I would look at rvarmor.com. I don't have this product, but it has great reviews and is much better and longer lasting than rubber.