:Does anyone know of a way to get rid of mites in a fruit fly colony without killing the flies?
The best way to get rid of the mites is to start a whole new colony. Make sure that your media is sterile as well as the jar containing the colony. If you re-introduce adult flies from the formerly infested colony, there will still be a slight chance that you may get mites again. I would suggest that you use filter paper(as in coffee filters)to be secured on top. The density of the filter paper should be sufficient to prevent any wandering mites getting back in to re-infest your "clean" colony. Goodluck.