In the scenario you described, thermal energy flows from the flask with hot water to the flask with room temperature water. This is because heat naturally transfers from areas of higher temperature (hot water) to areas of lower temperature (room temperature water) until thermal equilibrium is reached. The conductive metal bar facilitates this transfer of energy.
The picture below shows two flasks, one with hot water and one with room temperature water, which are connected by are a conductive metal bar. In which direction does the thermal energy between the flasks flow?
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