There are way too many variables to consider in this situation to be able to give you a definitive answer. Type of pollutant, solubility in water, airborne concentration in proximity to evaporator, exposure time, to name just a few. Syrup can certainly become “contaminated” with smoke and ash from the fire. I can attest to that from my early days. From what you describe I certainly would have dumped the batch,or at least stopped the boil and solved the problem.

Speaking of solving the problem, I wonder how the evaporator is producing so much uncontrolled waste heat that it is able to burn plywood and melt cement board. Are the grates open to the ground? Is it bricked and insulated?