usually the flux gets rid of itself by putting bad things into the environment.
Every time a wisp spawns, and every time a lightning bolt strikes- the flux is going down.
Pure Nodes reduce flux - these are the ones that grow inside silverwoods. You can combine pure nodes by planting a silverwood on top of one. So planting silverwoods and cutting them down and planting them again in the same spot should stack up a pretty large pure node.
As for the infernal furnace not working - I thought it stopped working when the aura ran out of vis - not filled up with flux.