I’m learning about this as you are, but some findings from the internet I have found is that Fluconazole (such as Reef Flux) is effective for treating certain types of algae, particularly cyanobacteria, but it can also impact other algae, including Chaetomorpha (cheato). While fluconazole doesn’t typically kill cheato outright, it can inhibit its growth, causing it to slow down or even die off in some cases. The degree of impact depends on the dosage, exposure time, and overall tank conditions.
If you're concerned about your cheato, it’s best to remove it temporarily from your tank or refugium while treating with fluconazole to avoid potential stress or growth issues. Alternatively, you can monitor it closely and adjust the dosage or treatment duration if you notice negative effects on your macroalgae