Unfortunately, I have dosed it with rock and substrate. I am just curious though, why do you believe it won't be eradicated? I understand that if there are eggs present in the rock/substrate , then the chloroquine could not penetrate the surface of the eggs, but the eggs cannot stay dormant for ever, and once they hatch, won't the cp kill any free swimming parasites, or at the very least, prevent them from living off any of the fish, or is there something I'm missing?
I believe rock/substrate absorbs CP (same as with copper), dropping it below therapeutic levels. At least with copper you can keep track of the absorption by using a test kit and dose more to compensate. No practical test kit exists for CP.

The rock/substrate probably leaches some of the medication back into the water (again, just like with copper), but who knows when/how much. I have nothing to back this theory up, except the countless failures I've read about where CP is dosed in a DT. I figure the main difference between using it in a DT vs. a bare-bottom, rockless QT (where I've had nothing but success with the medication) is the rock/substrate part of the equation.