The whole idea sounds scary to me.
In any case, when I get my barrels totally decoppered with my Outers Foul Out II, I don't get any false readings of copper presence from my jags. I don't think this is a problem. I think that if the patch still comes out with any blue, you still have copper in the barrel, probably in little pits from a rusted bore if it seems to take forever to get out.