I dont think it does anything bad. Cause when I change textures I just do that and it doesnt seem to mess anything up. I dont think your putting textures on top of the other. Your changing it not adding on top.
Applying a new texture replaces the old one, so you do not need to worry. Such a problem will only appear if you have 2 brushes in the same spot, and from your post I take it that that is not the case...