What may have happened is the roots might have gotten slightly damaged and the various organisms that cause roots to rot were able to enter the roots. Even if you use new water and new medium, these microorganisms can life harmlessly on the outside of roots, only causing issues when the root is damaged.
Letting the roots heal can involve potting the orchids into dry medium and waiting a few days to water or to pot the orchids the maximum exposure to air for a time (so that the roots dry very quickly after watering).
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