That is an awesome setup. Way to take advantage of the renovation period to find a very efficient way to heat the home. It's a weird problem running into the HVAC and the miners fighting each other for a stable temperature. I've never delved to deeply into the automation side or smart home systems. I would think though that you should be able to remove the home thermostat entirely from the equation for fan control. Have one upstairs that sends the heating/cooling demand to the fan circuits, and the main one is there to handle the house HVAC only. Maybe a different brand as you mention you think Ecobee is the issue there.
Thanks! My circuit will effectively be like what you mentioned - but more advanced. I will monitor the exterior temperature, the miner intake temperature, the temperature of the interior space being heated, and the temperature of the room the miner cabinet is located in - or the exhaust heat (toggle-able) if the room temp isn't an issue. This will allow for blending air from outside to keep the intake at proper temps if too cold - and with code changes and available relays also looping in cooling sources in warm weather. It will act as a thermostat for the interior heated space in terms of the miners. Just have to set the HVAC thermostat to heat just below and cool to just above. I will be integrating this with MQTT so as to allow some integration with home automation systems like OpenHAB for remote and dynamic adjustments as well as my only remote management site. The circuit will also have smoke detection built in so intake and exhaust sides of the miner cabinet can be monitored for smoke - allowing the circuit to power down everything. To be able to do that - it will also be able to turn on/off the miners via power relays. With the MQTT integration this would allow for remote shutdown and restart when software control to a miner cannot be gained remotely. Manual overrides on the circuit via push buttons and via the MQTT system to force airflow in whatever direction in preferred - outside or interior - or turning dynamic temperature control off - meaning fans blow outside, or and outright shut down. It's pretty cool! Most of this is already coded. I need to integrate the MQTT aspects and the intake blending - but the rest is done. The circuit is designed and the breadboard prototype is operational. It will have the main PCB and sub-PCBs for the remote temp/humidity sensors that will be connected via standard CAT5/5e/6 network cables with standard network wiring - so no special pin-outs. Sensors should be good out to around 200' if I recall properly (haven't looked for a bit on that spec).
I have more deeper areas to delve into on the home automation side as well - but MQTT helps with that as well.
Anyway - it has been a fun project and I'd say right now - between heat pump power and propane - it has saved us around $2500 dollars so far. I also put in a separate commercial service to the house - it REALLY cut down on the power bills. Home power is like $0.107/KWh and the commercial power feed is running a bit under $0.07/KWh. So right now - my S9's with stock firmware are still profitable even without the power and propane considerations on the home side. I'm still a happy camper at the moment!

Thanks @philipma1957! I just may get those. I have been buying low priced MERV 3/4 throw aways - at 12 for $36 - so that gets me to about $144 per year - so in a little over 1 year these would pay for themselves and they look like they would be easier to deal with as well. Do you use either of the cleaning/deodorizing sprays they suggest? Considering these do have the air coming into the home air space - what would be your though on these from your experience? That adds another $50 to the cost for these two sprays per what time frame...