The furnace runs,cycles, and puts out heat just fine.
Do the other appliances also work fine - water heater, stove, refrigerator?
I am not sure that the furnace could actually technically run through a full tank in such a short time, and still cycle / work correctly without any obvious side effects.
And I can not believe a leak big enough for this to happen could go unnoticed.
Are you positively sure that the tanks were actually empty? Is there a possibility they were filled with pure butane (which does not evaporate below freezing)?