In the movie "The Green Mile", John Coffey heals the prison guard Paul using his special power. He then opens his mouth and hundreds of "flies" appear buzzing away.
What are those flies supposed to represent?
The flies are a physical manifestation of disease and evil that John Coffey has sucked out of the body. (I'd have preferred them to fly away rather than dematerialise.)
Coffey also exhales insects after he cures the mouse with the broken back, so I don't think the flies can represent disease extracted from the person being cured.
My guess is the flies are something like the exhaust gas from a motor. Whatever mechanism Coffey uses to heal generates (psychic?) waste that he has to get rid of. However I can't find anywhere in ther book that goes into any more detail. In fact I can only find the two mentions of the flies.
The flies were representative of the demonic powers of Satan, Beelzebub to be precise - another name for Satan. Beelzebub means "lord of the flies"