I didn't have an algae scrubber running on my tank but if I remember correctly, either in this thread or one of the links, the possibility of fluconazole killing the algae on a scrubber was something to consider. Many have used the treatment to rid their tanks of other types of algae, mainly gha, so an algae scrubber is more than likely to be affected. It's possible that you might have to start all over again with your scrubber.
From the previous post I thought you had an algae reactor with chaeto. Now I see your situation. It's still going to be a hard call to stop treatment or to continue. Either way you may just have to start your algae scrubbers all over again.