Given they didn't announce anything in the patch notes or in the run up, best guess is you simply wont be earning them again and will instead be expected to just grind the red borders in the activities they are in. For the ones that don't have a grindable source but are in Xurs pool (ie Plunder weapons), I'm assuming that Xur will continue to have the ability to drop them as red border via his Strange Engram as they didn't mention his reputation track was removed.