I just "completed" fluconazole treatment from reef hd in my setup. My nutrients doubled by week 2, but they were very low to begin with and my bryopsis outbreak wasn't terrible. My phosphates went from .03 ppm to .06 ppm (via hanna ulr phosphorus). My nitrates went from 2 ppm to 5 ppm (via salifert and Giesmann).
The fluconazole completely removed the bryopsis in my system, which was mostly limited to my attached frag tank. I'm not sure if the nutrient levels were increased mainly because of the breakdown of algae or the fact that my skimmer wasn't collecting waste for 2 weeks? Now I am 3 days post treatment and 20% water change (approximately 250 gallon system) and my nutrients have decreased to .04 ppm phosphate and around 4 ppm nitrates.
I would think that in a smaller system with a really bad bryopsis and/or gha problem the nutrients would increase more dramatically. I would maybe be a little nervous if treating a neglected tank that has high nutrients with fluconazole. Probably a good idea to monitor nutrients more closely if this is the case, but if your tank is getting overrun with bryopsis there may not be much to lose.