Secondary Thermostat?

Hi, My programmable thermostat in the living room stopped working. I never liked it in there because of the extreme sun exposure. There is a manual thermostat on the second floor (split level) which I've never tried in 10 years living here. If it can turn on furnace, would it cause a possible problem even if the prog. stat is turned off with no batteries installed? It may sound like an obvious question, but I can't afford anymore expensive problems with this house! :wall: Note: I did purchase a new programmable, but it's going back because the face place won't separate from the base. Crazy. Thanks- R