I have a 2 story house one thermostat downstairs(does not have different zone settings), with one lennox merit series gas heat system. The unit has a synchron zone valve in the ductwork, air passes through first zone(downstairs) to get to second zone(upstairs). The zone valve opens when unit is turned off but stays closed when unit is turned on keeping heat from getting to upstairs. I took synchron motor out so it would stay open and keep both floors heated. What are some drawbacks of doing this? Or what can I do to fix system to work the way it is supposed to be designed? Any help would be greatly appreciated.

The zone control for the upstairs is only supposed to open when the upstairs calls for heat. Sounds like it is wired in reverse possibly due to a thermostat change with improper wiring,

If you only have one thermostat, there is really no need for a damper upstairs. I say you'll be just fine with keeping the upstairs damper open as you've done.

I tried leaving the damper open last night and it way to hot upstairs and not hot enough downstairs. I do think they wired the thermostat wrong. It looks like it is a thermostat that is only designed for one zone. I bought a thermostat that is designed for a 2 stage baffle system. But I notice it has a w2 slot for the baffle for heat and a y2 for the baffle when on a/c but I only have one wire running to the baffle. I have it connected to w2 for now since we are running heat but not sure if I will need to run anything to y2 for a/c in summer? Also not all to sure this is going to work right, I will have to see tonight if it kicks in. How does it know when to kick heat off for upstairs without a thermostat?

To have a true 2 zone setup using the design you have you need to have 2 separate thermostats with each one installed in the area for which it serves.

It seems to me you have a few pieces of your control system missing as far as I can tell. Your best bet at this time is to call local for a on site HVAC repair person since we cannot really see what you have from here.

As you mentioned leaving a damper opened especially one going upstairs where the heat accumulates naturally does not work and doing that can turn the area into an oven in short order. Adjustments to the furnace controls might also be necessary and that is another reason to get on site help with this situation.