Last Sunday, I did a substrate change on my 31G. I changed gravel to Flourite. I took out all the fish and put them in a container. Once I finished changing the substrate, I add the water back in, add some Zeo-Carb into the filter. I put the fish and plants back in. I checked ammonia, it was very very low, not harmful to the fish at all. I also checked nitrite, it was very low too, so I don't have to worry about them. I think the Zeo-Carb will solve your problem. Also, you should add some Bio media into the filter.