A decontamination flash is a flash of light and radiation which decontaminates whatever is being flashed - supplies, food, or sapients. It is generally agreed by several species (Human, Aandrisk, Aeluon at least and, by extension AI) to be a very unpleasant experience, but fortunately does not take very long.
They are often used when a visitor's immubots are not aware of threats posed to other members of the crew by diseases which don't affect the visitor carrying them.
Possible effects of having one include drowsiness, vomiting and other unpleasant things.
Rosemary gets one when she boards the wayfarer, as do other visitors.