YOu might want to sprinkle baking soda all over the unrolled mats , leave for half an hour or so, then vaccum it all off. THe baking soda absorbs smell. Another way might be proffesional steam cleaning, but you would have to leave them out to dry.
We had the same iisue when we used to put up/take down the gym each tiem.
We did cover a beam, bought the whole kit from speith anderson, it is a two person job for sure, but not that complicated.