I changed out my substrate completely in my 10g (I had about 2 - 3" of gravel before) and had a full fish load, and didn't get any measurable quantities of ammonia or nitrite afterwards. I held off forever on doing it because I didn't want to end up re-cycling my tank because I had fry, but it didn't have to cycle again anyway. Plus that ended my bga issues so all in all I was quite happy that I did it.