I'm not really sure if this would work, but I've seen it done for removing mites from Malagasy hissing roaches... You could try setting up a new container for the adult beetles with fresh food medium, then individually take each beetle and run it under a burst of water from a sink or something. Hold the beetle and let the water push over it for several seconds, dry the beetle by dabbing it on paper towel, then place it into the new container.

The hope is that the stream of water will remove any mites that are on the beetles. Then by placing them into fresh media, you won't have re-colonization of mites... hopefully.

Or, you could get a new flour beetle culture, and cull this one. lol