Changing substrate

Question
A while back, on the advice of experts here, I covered my white pebble substrate with a thin black gravel layer to improve the color of the fishes. It worked GREAT and the fishes look much better now..
Problem is, since the dark layer is quite thin and the black gravel is smaller in size than the underlying pebbles, everytime I try to do some redecorating that involves digging in the substrate or, more importantly, gravel vacuum the top black gravel tends to move down bringing up the bottom 'whites'. Now I can't add too much of the black gravel cause that will make the substrate too thick which, I've heard, is not recommended unless its a planted tank.
So, I was thinking, what if I take out the white pebbles completely leaving only the black gravel.. Let's say I change one small portion (about 5-10 % of the total surface area) at a time and give a few days gap before the next. Will doing this ensure the 'biological balance' is not broken while changing the substrate ? If not, is there any other way this can be done ?

Answer
Removing the gravel will upset the biological balance. If you take a small portion every week to two weeks, it should not upset it too much. Just make sure you do not do it too fast. Also, moving the gravel will make the water very dirty since you are removing it from the tank. Make sure you vacuum the gravel first to minimize this problem.