What happened to my Green Chromis?

[Aquattro]

I don't think CO2 levels were the cause. More likely a too rapid shift in chemistry, CO2 easily gasses out of solution if you have decent agitation of the surface, and the lids aren't going to reduce this reaction. If you took the total area of gaps between the lid and tank, you'd likely have enough square footage to put your hand thru, thus more than enough air would be available to the surface of the water.
Also, that much CO2 (required to suffocate fish) would have given a huge drop in pH, which in turn would have shown as a much more serious problem. And the first sign of 02 deprivation is all your fish gulping air from the surface. (which isn't the case, right?)