I don't know the plant, so I can only point out two facts: 1) not every antifungal compound is effective against every fungal strain and 2) some antifungals are volatile and they may decrease in concentration during drying. If this is the case, maybe you can extract them with an organic compound when fresh. Something that you can separate from whater by centrifugation. Fragrance industry has many methods to do this. However, the first option is more likely. They get a mold that resist these antifungals.
Contamination with fungi at the time of drying is already an important indicator and therefore reportable. It is therefore important to evaluate the deposition and survival of fungi during these processes.
You may try freeze-drying in a speed-vacuum concentrator. As the drying process is run in a vacuum condition so it may help to minimise air-borne microbes.