You should not switch off the filter. You will cause the nitrifying bacteria in the filter to be starved of O2 and die off.
What type of filter do you have? Unless you have a wet-dry type of filter, you should not experience too much CO2 loss, if any at all, caused by the filter.
Water movement itself has no effect on the CO2 loss. It is the agitation at the interface between the water and atmosphere that accelarate the CO2 loss to the atmosphere.
In wet-dry system, e.g. sump filter, overhead filter, the filter provide lots of interface of contact between the atmosphere and water to provide aeration to the water for the bacteria. Gas exchange takes place at the interface, CO2 out of the water and O2 into the water.
In internal filters or canister filters, there is no interface. So no gas exchange take place in the filter. The filter rely on water intake to bring in O2 rich water for the bacteria. That's why one should not turn off the filter for prolong period.
BC
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