I'm not sure much can be done to prolong the life of a rubber roof. I have seen people with rubber roofs that have never been touched with anything to do with "clean" and they lasted 10-15 years or more. Some of them were black with whatever that is and even had moss growing on them and they still seemed to work. I tried to clean my roof a couple of times a year with some detergent and a soft brush and after 5 years the roof membrane started to leak through the membrane where the a/c's dripped. This was happening at both a/c's. So I replaced the roof with something more permanent in my opinion. rvroof.com was my solution. Not cheap, but no more worries about the rubber roof or caulking. And it was no more expensive than replacing the rubber roof that had failed.
2006 GMC 2500HD CCSB 4x4 Duramax/Allison, Titan 52 gallon fuel tank, Prodigy Controller, B&W Companion Hitch
2010 Jayco Designer 35RLTS, Cummins/Onan RV QG 5500 EVAP, Progressive Industries EMS-PT50C, TST Systems 507 TPMS, RV Flex Armor Roof