That's why I like a CC base. If you use CC, don't try to use it to remove nitrate. Instead use LR or other means of denitrification. Because you are keeping a shallow CC base, it won't house anaerobic bacteria. The CC will remain high in oxygen and therefore if you move things around, it won't crash the system.
It's anaerobic bacteria that causes a system crash. When anaerobic bacteria is exposed to oxygen, it dies. Then you have nothing left to complete the nitrogen cycle and nitrates will go through the roof. Anaerobic bacteria are good, but you have to be carefull not to kill it. Distrurbing a DSB is what kills this bacteria. If you instead use LR, you CAN'T kill this anaerobic bacteria. This is because the bacteria will colonise mostly in the rock, rather than the substrate because you are using a shallow CC base that is oxygen rich.
In other words, if wastes are present in the system, bacteria will want to form. Either it will form in the substrate or it will form in the LR. If you don't let it form in the substrate, it will prefer the LR instead. Now that the bacteria is colonised in your LR, your substrate is safe to move around and mix as you chose and the anaerobic bacteria will be protected by the porus nature of the LR.
I probably need to write an article on using CC properly because it seems like most people are unfamiliar with it and becasuse they tried to use it like a DSB, they only had problems and are now convinced that CC is bad. Well, it's not. I would say that it's actually a lot better. You just have to approach filtering your tank differently and have to discard the mindset of using the substrate for denitrification.