I have a Mastertrol Mini Zone-2 heating system. One of the Zones stopped working. I checked the non working damper by wiring to the working zone and it worked; so the damper is not the issue. What would cause the 2nd zone not to work properly

It could be the t'stat for that zone or the control board. You eliminated the damper, good sleuthing. Look at the control panel, there is usually a wiring diagram and it may show voltage test points. Is the zone light green?