Assumptions: Essentially all oxygen that's ever been present in the atmosphere originated from oxygenic photosynthesis. The production of an oxygen molecule during photosynthesis leads to the consumption of a carbon dioxide molecule. Likewise, we assume that the principal consumer of O2 is the oxidation of carbon (e.g. through respiration or combustion), in which the consumption of an O2 molecule requires the production of a CO2 molecule. Therefore, without an external source or sink of CO2, any increase in O2 requires an equivalent decrease in CO2, and vice versa.
We know that O2 levels rose to ~30% of the total atmosphere during the Carboniferous era. Thus, O2 levels fell by 9% in the 350 million years that followed. This appears to require a concomitant increase in CO2 of 9%, by the assumptions above. Given that the current concentration of CO2 is merely 0.04%, where did all the CO2 go?