Has Earth's atmosphere lost mass throughout the geological ages due to biological $\small\sf{CO_2}$ fixation?
Yes, the Earth's atmosphere has thinned in the past few billion years, and biological fixation of CO2 was one of the main causes. It also gave us our present abundance of oxygen (21%). Enormous quantities of CO2 were used in the form of CaCO3 by foraminifera, corals etc to make their hard skeletons, and the resulting sediments formed limestone. Other elements formed compounds with carbonic acid (CO2 + H2O) to create other carbonate rocks.

In addition there is the more obvious sequestration of CO2 which was taken from the atmosphere by photosynthetic organisms and buried underground in the form of fossil hydrocarbons (oil, coal, gas, lignite etc). It was this which gave us our all-important oxygen. So the answer to your question is that biological activity has done both. It has hugely reduced the mass of the Earth's atmosphere, and at the same time greatly altered its composition.

It is also worth noting that the Earth loses substantial quantities of atmospheric gases into space, mostly hydrogen, but other gases as well. The bombardment of the outer atmosphere by ultraviolet rays, cosmic rays and the solar wind plays a part in this.