CO2 uptake from plants in a compressed system is negligible. I did the math in another thread a while back; 1-3% at very most turns into plant.
I can't find the thread where I did those numbers, but I can give the basic concept well enough off the top of my head/with a little reference. Plants max out at 50% carbon by dry weight, dry weight is about 1/10th wet (on the high side). Because of this plant growth maxes out at about 20x carbon weight. CO2 is 27% carbon, so you'd need 74mg/g co2/wet weight to produce 1g of your average-ish macrophyte material. Now, a 5lb CO2 cylinder does a 20 gal for about 6 months; We'll call this 12g a day of use. That's 162g of wet weight per day, 2.5lbs of wet growth per week. Now go to your grocery store, and look at the little 4oz boxes of fresh herbs; that's ~100g. Most of us might grow that out of 20 gal in 10-14 days at fastest, any significantly higher number would require going through CO2 faster to keep balance with the light.
I'm betting heavy pruning eliminates low-CO2 areas where there's reduced flow/distribution. Pruning plants can also make for a big mess in the filter if you aren't turning it off and netting out all of the clippings, which would cause an NH4 dump. Osmotic shock isn't a bad guess either. I'd check your KH rather than pH; it's a more direct indicator, and any NH4 present won't throw it off.
