Some has reported that only algae exposed to light (talking about briopsys) die. This could be valid for cheto too; so leaving it w/o light could be an option. It also advised to treat the whole system, algae refugium included, because it could reseed the DT with briopsys. Anyway if we don't illuminate algae, they don't die. So it's a hard choice.
Maybe waiting for the system to mature could be the best and natural option, but I think it is necessary to have all the fundamental elements needed by all the organisms. In my DT, the never cleaned parts of pipes, glasses and pumps got naturally cleaned from briopsys and got covered with coralline algae.
Luca