with all the ideas that you guys have gave me this is what im going to try.
1st step wash as much roots out as posable
2nd step boil in a 10gal turkey fryer
3rd step bake in the oven to dry
ive done a 50L bag so far it sucks but its better than just buying new.
I'd eliminate either step 2 or step 3. both would do the same thing, kill anything organic so it can be rinsed off easily.
maybe if baking seems easier than boiling, do a search to see how people bake them. I'd put them in a giant pan and bake them for 20 minutes at the highest temp that the oven would go... 500 or so. Shouldnt take long to cook any root matter at that temp, plus, all charred up, it should rinse off easily.
2nd edit: why not just try a cookie sheet and a pan to boil, to test each method. Clean small amounts of pebbles, but try to get nice and dirty/rooty pebbles. Rooty Pebbles!! lol , get it?
seriously though, before you go through some major process with such a large volume of hydroton, give each method a test run, hell, you can do both at the same time and see which ones seem to come cleaner. Even do a cookie sheet of 'pre-rinsed' hydroton, and another with the stuff sraight from your ebb/grow. same with the boiling. Time is money. Good luck and please post results.
Upon further thought... skip step one too. Why bother going through that lengthy step if you're just going to boil or bake the fuck out of the old roots anyway? burn the shit the fuck up and rinse it the fuck off. BAM! clean clay pebbles. (or so we all hope)