The house had a two-zone heat/cool system, with two non-programmable thermostats (round ones).
I replaced the MASTER thermostat with the Honeywell RTH6400 (programmable). It seems to work fine.
However, the old thermostat had two wires too many to be accommodated in the new one, so I left them unattached, as suggested in the installation booklet. Now, the SLAVE (upstairs) thermostat does not seem to work - I guess it needed those two orphan wires after all.
I tried to seek advice in the store, but no luck.
Do I need a special two-zone thermostat? Or, should I pair the extra wires with some other wires that have a connector in the new thermostat? If so, which ones should be paired?
Grateful for any guidance.

Exact brand and model number of old thermostats.

Exact brand and model number of old thermostats.

Thank you! Sorry for the delay - I cannot find the thermostat I removed... I believe it was a regular round Honeywell thing.
The SLAVE upstairs thermostat that is not working now is a Robershaw, and it has a glass vial (mercury?) inside.
The two "homeless" wires coming to the MASTER thermostat were connected to O (Q?) and E connectors of the old replaced master thermostat. The new Honeywell programmable thermostat does not have receptacles for these wires.
I very much hope that this information will allow you to give me your guidance. Thank you!

I would try to find that old thermostat because the one you have now will probably not work and I would like to know the EXACT part number for the old thermostat so I can try to find a modern replacement.

The dual control systems can have many different styles and controls. Some have dampers in the duct etc. Without the old exact model number it can be a problem.

I would try to find that old thermostat because the one you have now will probably not work and I would like to know the EXACT part number for the old thermostat so I can try to find a modern replacement.

The dual control systems can have many different styles and controls. Some have dampers in the duct etc. Without the old exact model number it can be a problem.

Thank you. I was able to find it, and it is indeed a Honeywell but not a simple one: it contains mercury. I am not sure which one of the many markings on it is the model/part number, so I list all I can see: LR 1620; T87F 2873 3 0239; Q539A1436 MCRS.
Again, I am very grateful for your guidance.

Some info for you

http://customer.honeywell.com/techlit/pdf/PackedLit/69-0536.pdf


Your system was a zoned system and requires thermostats that will not only work with the system but also the dampers installed in the system.

Before any damage is done I suggest you have a ON SITE service performed to figure out exactly what you have and what new thermostats will work with your system.

These systems work well but can be a pain in the A$$ to work on especially when you are trying to up grade. Sorry to be of little help except to send you in the correct direction. Damage can result to your system controls by improper hookup.

Thank you, will do accordingly.