From my understanding, you will want to keep the concentration of fluconazole relative to the amount of water in your tank more or less the same, so after the water change, add back in a dosage of fluconazole equal to the amount you took out.
However, when I dosed my tank I did a 25% water change midway through the decline of the bryopsis and the little bit of green hair algae I had and it still ended up killing all of the nuisance algae in my tank, save for the little bit of green cyano or slime algae that popped up, I did not replace any of the fluconazole I took out. We have seen that fluconazole doesn't appear to have any negative impacts on reef aquaria life, so I think replacing what you take out from a concentration standpoint is a safe choice to make.