The CO2 is consumed by the food plants. This is part of the carbon cycle, assumed that all food is grown by food plants in the colony. All hydrocarbon intake is exhaled as CO2 after digestion and metabolizing. Exactly the same amount of CO2 is inhaled by the food plants and metabolized to hydrocarbons. The carbon is neither created nor destroyed anywhere in the cycle.
The photo synthesis basically creates glucose from CO2 and water:
6 CO2 + 6 H2O → C6H12O6
The settlers basically metabolize the glucose and release CO2 and water:
C6H12O6 → 6 CO2 + 6 H2O