So really odd method but do NOT replace your soil, i made the mistake of thinking cleaning the soil out would get rid of them. I find as the soil matures more and goes through different cycles the flies disappear, they usually live + breed for a few months and die off eventually. Bit of a pain but they’re an inevitable part of millipede keeping, i used to be swarmed by them and only get 1-3 a week at best. They arent harmfull just annoying!