Baking soda will deactivate chlorous acid, but it will not have any effect on the free chlorine dioxide in the solution. It is all dependent upon the PH of the solution. If the PH is too acidic, you damage your teeth. If the PH becomes alkaline, you deactivate the chlorous acid. The goal is to have the PH very slightly acidic.
The normal mouthwash is alkaline. If there are any acids in your mouth, they activate the solution as needed.