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I am no expert, but I think you are suffering low oxygen levels
rather than co2 poisoning. It took some thought for me to finally learn
that co2 and o2 concentrations are at best indirectly related; measuring
one never gives conclusive evidence of the others quantity.
Sounds like you prune and change water in the evening, have you
tried to do it in the morning? This might allow your plants an opportunity
to run up oxygen concentrations before the lights go out. I have also
noticed plants bleed bubbles for a few hours after pruning perhaps creating
a need to draw more oxygen out of the water at night.