If the cultural conditions are corrected,as you did and are doing,a single good soak with fungicide should suffice to immediately halt the fungus and the good culture will take care of any surviving fungus. If the plant is very valuable to you and dont want any risk of fungal progress at all,you could apply at each watering but,although that will certainly stop the fungus,the plant growth rate will also be affected negatively from the fungicide. It comes as a side effect and can even halt the plant growth for a while.
Oncidium root and grow fine even when kept dry and watered periodically,so leaving them drier,even with a small root system,wont hurt them. If some of the roots reach deep enough to be in moist pellets,no watering is needed even with the roots above being dry for prolonged periods,they will still grow. If no root reaches deep enough,you need to water those every few days,a day after all roots are fully dry. Just make sure the pseudobulbs dont shrink too much. If they do shrink,just water more often but with very good air circulation afterwords.
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