If this was me I would remove all of the old sealant, clean the roof and replace with new sealant. You can use different sealants for this purpose such as Dicor lap sealant or Eternabond tape. Unless the rubber roof has been damaged and or the skylight its self has been damaged. Then you need to address those issues separately.
2016 34RL CC; 2008 Ram Mega Cab 2500HD, 6.7L, 68RFE 6 speed, 4X4, Smarty S67, TDR 135K+miles