I wouldn't run the furnace with a blocked duct. It probably (but not for sure) won't start a fire but you start creating big temperature differentials that can warp things.
More importantly, it's unlikely to do enough going down the road at 60mph. Windchill will quickly cool the tanks and will blow away any residual heat off the ducts.
As others have said, pick another time to "clean" the tanks or dump some antifreeze in. Reality is you aren't going to do much cleaning unless you drive like a maniac or go off roading with the trailer. Just cruising down a smooth freeway, the water is just going to sit in place.
