Air Gap

Ok, I fired up for the first time sunday night. Both furnances worked awesome. the air was very warm coming out of the floor registers. Tuesday morning one was blowing cold air and the other lukewarm air. I manually bled off the vents and got some air. Water pipe was cold going into and out of valve going to exchanger. So I shut off circ pump, opened check vavle and boiler drain and opened up the auto fill valve all the way and let run for 10 minutes or so. One furnance is blowing hot air the other is blowing lukewarm air, like out of a heat pump. The supply side going into exchanger is hot, and touchable on return side. When I purged I did not manually open valve going into exchanger. So is it possible I still have some air in the actual exchanger. If so will it eventually work it's way out?

You need to open all valves before the heat exchanger to purge it.