They did bring tons of comet with them. Which could theoretically be a source of carbon. It's a stretch, of course. But I think the story was that they kept the population in the Cleft down to a few hundred for many generations, only growing beyond that once people began venturing further afield. At that point, carbonaceous asteroids are not implausibly hard to get -- from high orbit, you've already paid most of the delta V needed to get elsewhere in the inner solar system, if you've got a lot of time to spend.