I know this post is old but for anyone who comes across it. A few people said to clean with a flushing agent but for the most part all that stuff is just empty chelates that help the plant eat up everything in the root zone then after that you would flush with just water to finish. That doesnt help clean hydroton unless maybe theres a soap added like in royal flush, and even then I wouldnt waste the product on it. Someone else said not to use bleech because its a salt. I have to say Im pretty sick of all these salt snobs. Bleech is awesome because it absolutely kills everything and not that I would compare bleech to nutes but what excactly is it you organic nuts think plants eat. They eat inorganic mineral salts. The only difference is how they get them. If your having trouble with large amounts of hydroton I would swich to smaller nets that hold less. The only problem with having more roots exposed to the water though is root infection unless you have a chiller, use mycorrhizae and zyme or dont use any organic stuff at all. As far as cleaning go's if you have alot of plant matter in the hydroton I would soak it in zyme and then clean with bleach after. If your not using mycorrhizae and zyme in your hydro system you want to make sure to get rid of as much organic matter from the hydroton as possible and than purify it good. Zyme and then bleech does that nicely. I have an ebb and flow but instead of using the full inserts that come with it I use smaller 6 inch ones and its amazing how much less hydroton you use. When cleaning I take the full size nets filled with dirty hydroton and put those in five gallon buckets filled with water and zyme. I let that sit untill the zyme breaks down anything left over and then I soak with bleech and rinse very very very well. One full insert of hydroton gets me six 6" small inserts so its alot less to deal with. If you go with the smaller inserts just remember that its easier to get root infections when more of the roots are completely exposed to the water like in a dwc system. Either just use base nutes and h2o2 with absolutly no organic additives or get rid of the h2o2 and use mycorrhizae and zyme. You could also get a chiller but they are realy expensive and as long as you keep clean and either use h2o2 with no organic additives or use mycorrhizae and zyme you should be ok.

Opie Yutts idea sounds good too if you dont have the money for zyme and can stand spending a little more time messing with the hydroton. I might try that method next time.