I doubt the thermostat wire runs thru the furnace and then to the a/c. The furnace and a/c are controlled by the same thermostat but different circuits are used for each device.
Are you trying to physically delete the furnace from the TT? If so, you should be able to simply remove it, tape or otherwise insulate any bare thermostat wires in the furnace compartment and be good to go. Unless you have some kind of non-standard cobbled together system.
Again, if you could provide information we could provide a more educated response. TT model, a/c model, furnace model, thermostat type. Anything would help.