Most of my base rock has 100's of unwanted zoos on them. Can I remove the rock, scrub the hell out of it, and put it back in the tank without any problems? Or will there be some kind of cycle?
+1
scrub them out of the tank, rinse them REALLY well with tank water before putting them back in the tank.
I would also run carbon aggressively for a while afterward if you don't already. I'm not even sure that that will suck up toxins, but I get the sense it can't hurt and could very well help.