Fungicide will kill many of the probiotic organisms. You can't flush it all out. The idea of prophylactic spraying for disease has been discredited; it kills beneficial organisms that keep the fungi under control, and selects for pathogens resistant to the fungicides used. These are the same reasons the general human population should not routinely take antibiotics to prevent infections.
Windowsill growers will only rarely need fungicides. The only pathogen issues I've had have been Phalaenopsis crown rot in plants I kept too cool in winter, and Erwinia in Phals that were too hot and humid when I couldn't get into my growing area for several weeks. I successfully treated the survivors with hydrogen peroxide in the crown, not on the roots.
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