I don’t think the earth tube is simulating the impact of it’s inflow air with respect to the conservation of mass in the zone. The AFN does conserve mass, using it’s pressure network, but, from what I’m reading in the Engineering Reference, the earth tube only estimates volumetric air flow in the tube, and then EnergyPlus assumes the sensible and latent heat from the earth tube’s volume of air is combined with the room air conditions (same as convective, infiltration and simple ventilation heat transfer in EP).
Why not just keep track of the thermal energy balance instead? You should be able to see the relative impact of this additional heat transfer on the zone energy demand for both rooms.
Are you trying to model the heat exchange between air flows from different sources spatially (i.e. tracking mass and heat changes for naturally ventilated buoyant air through zones)? You may want to look at Salmaan Craig’s work, I recall he built some custom tools to model the heat transfer due to buoyant air flows in zones. Can’t find a link to it, but here’s his google scholar page: Salmaan Craig, Eng.D - Google Scholar.