If you do regular (weekly) water changes, the aquarium water and tap water should have similar water chemistry values (GH, KH, pH). So doing a large water change (75-80%) won't harm the fish as long as the new water has a similar temperature to the aquarium water, and the new water is free of chlorine/ chloramine before it's added to the tank.
The substrate might not be releasing anything now but there might be gunk trapped in it that could be contributing to skin irritation. Gravel cleaning the substrate at least once a month would help remove a lot of the harmful disease organisms that live in rotting fish waste.