In the old vial (the one with flies in it), gently tap the flies down by softly tamping the vial on a soft surface, such as a mouse pad. The flies will fall to the bottom and remain there for a few seconds (no more than that!), enough time to quickly take the plug off the vial, invert it into the funnel, and gently tamp, together, the two vials to force flies down into the new vial.