I've done flux before, but I took a few steps to help out the corals: added a bubbler, dosed PNS Probio and Fiji Mud (now switched to Aquaforest Life Source) and checked nutrients more frequently. I've had a monti and an RFA change colors a bit, but otherwise nothing else affected.
Beware, fire and brimstone preaching on the way. Turn back now!
In principle, it should not do much of anything to corals since it acts primarily against the process of fungal cell wall developement, for which algal cell wall developement seems sufficiently similar. Corals and other animals do not have cell walls, although they do have similar target proteins (cytochrome P450). Humans take fluconazole for fungal infections and do experience side effects, so it can for sure affect higher organisms, but as is often the case, this seems to occur in a dose-dependent manner, and the doses used in humans are so much higher than what you use for algae in a fish tank, I venture a guess that it won't cause toxicity to your corals. That said, killing a lot of organisms (algae) in a tank can have downstream effects. I would imagine that more stuff killed and the faster it's killed, the more potential for nasty side effects. For example, what happens to the space left behind? If nothing is ready to take its place and the unspent nutrients are available, I'd venture that its a good opportunity for dinos, cyano or other bothersome stuff to take resistance. My hope is that the Fiji Mud and PNS Probio help fill that space. Nutrient release and other processes of algal cell death might affect water parameters. Maybe oxygenation? My hope is that the bubbler counteracts that if it occurs (and if not, isn't harmful in any case). Nutrient swings can also affect your corals, so keeping tabs on that helps, and the PNS Probio might help with nutrient management. There are plenty of other ways to manage nutrients.
One thing I'll do whenever there's time (like, never, unless I reduce my reef2reef postings, HA!) is look up the alignments of P450 in fungi, algae, coral, nems, snails, crabs, worms, fish and humans to look at homology.
Anyway, I plan to use flux again because the bubble algae is on the rise, but it isn't in plague proportions, so hoping it goes easily without much perturbance to the system. Also, I hate bubble algae.
