If that's the case, it's an easy fix. Just have it so it removes blocks one at a time starting from the top instead of the bottom. Either that or have the fill set a priority for specific blocks.
Anyways, if the problem is because it goes one at a time, then I can implement a work around for my project. Instead of filling the space with air, first fill with barrier blocks, then fill with air.
If that's the case, it's an easy fix. Just have it so it removes blocks one at a time starting from the top instead of the bottom. Either that or have the fill set a priority for specific blocks.
Anyways, if the problem is because it goes one at a time, then I can implement a work around for my project. Instead of filling the space with air, first fill with barrier blocks, then fill with air.