The popular wisdom that you'll often see here in RC is that bio-balls are "nitrate factories." Some people say that they run a sump with bio-balls successfully, though. Still, IF you have a reef with coral that are more sensitive to nitrates than fish are, it's a good idea to remove the bio-balls. That's premised on whether or not you have a "sufficiant" amount of live rock in the tank and whether or not you have a good quality, effective protein skimmer as well. If you have the rock and the skimmer, then, IMO, there's no need for the bio-balls and I'd take them out. If you have a fish only tank, then I don't think there's any reason to be concerned about the bio-balls and you can leave them in the sump.
If you decide to take out the bio-balls, you needn't replace them with anything. If you wanted to, but it isn't critical, you could put some live rock in the compartment where the bio-balls had been. A good idea, though, is to put an appropriate light over that section and put some macro-algae like Chaeto in there. This would serve as a "refugium," and foster a pod population and it would serve to consume any excess nitrates and phosphates.