Yea i didn't know what to do with my wet/dry sump space so i put these in thinking they would act like additional live rock surface area.
When you say put them back in but clean a quarter of them - should I put them all back in at once after I clean them?
You are right, they do act like additional live rock so that much is good. They just require some occasional maintenance is all.
If you clean them all at once or not depends on how you clean them and how much live rock you have.
If you have plenty in the tank I have found that cleaning them all at once doesn't mess things up. I always recommend doing them in parts just to be on the safe side.
If you clean them in salt water then the impact on the bacteria is less. I get a power head, put it in, and just blast them hard with it. The idea is to make sure the little center is cleaned out and any small bits of detritus is removed from the porous material.
Of course you don't "clean" them in terms of scrubbing hard or using a chemical cleaning agent. The idea is just to get the excess crap off. Whenever you mess with these things some bacteria will die off.
That said-based on the size of your tank and the fact you have well established live rock, I think cleaning them all or half would be good. Just don't forget to clean out that area of the sump while you are at it.
I have had this same issue in the past and this is what I did. I always throw in the disclaimer that since I can't see your tank and don't know any more of its history than what you have told me I could be wrong so ultimately you have to decide based on what you know. From my perspective out here in cyberland it sounds to me just like the ceramics are the issue.