If your effluent from the Reactor is plugged and CO2 is contiunously going into the reaction chamber the pH will nose dive and your substrate will break down more rapidly. Further more, when you open the effluent the pressure decrease will cause the CO2 to be released from the water collumn, like opening a soda bottle that's been shaken.
Occasionally, my effluent gets clogged and this happens. When it does, I just close off the CO2, and unclog the effluent. Then I let water flush thru the reaction chamber for a few days. Initially it clouds my water up. But, I have about 285 gallons so the pH swing is rapidly normalized.
In your 90, i'd just do the same, depending on the size of your reactor. BUT, that's just me. Others may recommend against it. I suppose the potential for harm is there with the pH swing. I've done it many many times without ill effects.
IF you were refering to your tank being acutely cloudy, and NOT your reactor, then I vote for a snail spawn. Whip up some water and do a water change at your earliest convenience.