2 common wires, 1 thermostat

My home has a separate heating and cooling system; I have hot water baseboard heating and central air conditioning. There is an R and W wire coming from my heating system, and RC, Y, G and C come from my air conditioning. The ecobee3 thermostat (along with the Nest and the Lyric) needs a constant 24v to run the thermostat, which it gets from the RC terminal, and the C terminal completes the circuit. I have a unique problem that I can’t seem to find a good solution to. I lose power in my area sometimes during October/November because of hurricanes and I have the most essential circuits in my home hooked up to a transfer switch which is ran by a generator… one of which is my heating system. The problem I run into is that if I were to lose power there would be no power going to the air conditioning transformer anymore because I don’t have the A/C as an essential circuit, so despite me having the heating system on generator, the thermostat wouldn’t work. I was going to just disconnect the common from the A/C and run a common wire from the heating system, but ecobee support informed me that when there is power from the RC wire and the RH wire, it will always use the RC wire. Being that I have 2 separate transformers for the heating and A/C units, during the summer when the A/C is on it would try and pull power from the RC wire and return it via the common wire now going to the heating system. That won’t work, I can't take 24v from one transformer and return it to another. I’ve spoken with ecobee support and after throwing some ideas back and forth the only 2 options he came up with were to use 2 thermostats, or hook up a backup UPS to the A/C system (which would cost way too much and is unreasonable to just run a thermostat). I asked both my HVAC contractors that installed my boiler and my A/C but they didn't really know a good answer. I have come up with an idea, but I wanted to bounce it off someone who knows more than I do. Note: The thermostat termination block in the below pic is my current Honeywell thermostat, I just used it as a reference. Image: http://i261.photobucket.com/albums/ii79/JCab85/Thermostat/hvac%20with%20toggle.jpg I want to run the common from the A/C and the common from the heat to a toggle switch. It’s a lot of work, but I would be able to have a common wire to both systems, and I could choose to use the common from either one. During normal operation the toggle switch could be positioned to have the common wire run back to the A/C, but when the power goes out and the A/C has no power the backup generator can supply...