The CYA test, if you're using the disappearing black dot test, could be lower in clear water than in cloudy water, since the test relies on turbidity (cloudiness) of the water to obscure the dot.

Check the manual for your SWCG--each unit specifies what the CYA levels should be. If you don't have the correct CYA levels, the unit has to work harder to maintain the chlorine in the pool, and that will cause your cell life to be shortened, so you'll have to replace it sooner. Also, it makes it very difficult for the unit to keep a consistent level of chlorine in the pool, leaving you more susceptible to algae outbreaks.

Janet