IMHO get rid of the rubber completely. It will leak somewhere sometime. I replaced my failed rubber roof in January 2016 with RV Flex Armor. Expensive yes, but about the same price is a replacement rubber roof and there are zero caulking joints to constantly monitor and wonder when a leak will happen at a spot you missed. My roof is completely zero maintenance except for an occasional washing with Dawn and a soft brush if I want the dirt gone. Another benefit is the RV Flex Armor roof is 3/16" thick which ads some insulation benefit as well as sound from hard rain. I am hearing impaired and I can now hear my television even during hard rain storms.
Would I make this change again? Yes, and I would do it immediately on a brand new unit before I ever used it.