Ick. Sad to read about this.
Here are my first thoughts.
How big is the coop? Can you upload a photo? How much and what kind of bedding do you use?
Borax is a natural, non-volatile anti-fungal. You don't want the ducks ingesting it, but you could dissolve some in water and dab that on the walls. I've used it on the wall behind my refrigerator, during the Summer of Fungi a few years ago. Shudder.
Seriously, I've used borax solution on truck carpets, walls, and fabric. It keeps mildewy things from coming back for quite some time. As I wrote, you just don't want to spill the powder or solution on the ducks' bedding where they could nibble it, but it won't make fumes that can hurt them.
It also discourages some bugs.