Adding the sand on top of the cc
would be a very risky thing to do. What would happen is detritus/food etc would find its way down and eventually start to clog the gaps in the cc
. Like you said the burrowing critters can't handle the coarseness of the cc
so there's no way to keep it clean under all that sand. It's also possible that the lack of turnover at the bottom would create a sulphide trap and then you're really in big doo doo.
You won't need to worry about losing bacteria if you change the substrate bit by bit over a long period, especially if you have plenty of LR