yes light fertilizer in all the water. otherwise your just going to delute what you gave them. I use about 1/2 teaspoon for the 1 tablespoon per gallon fertilizer.
When repotting a plant already established in semi-hydro culture, you should be unpotting, plopping the plant and medium into a new pot, then filling it the void space with fresh medium - in other words, no disturbance of the root system or change in the root zone conditions, so just keep on keeping on.