The only time you should empty the barrel of your machine is when you are preparing to remove the screw.
When discussing purging with most injection molders, the first step they follow is to empty the barrel of material. This practice is much less common in both extrusion and blow molding, but for some reason is commonplace with injection molders.
Once you empty the barrel it becomes a hot air oven which bakes all left over material directly to the screw. This also removes all pressure in the barrel when the next material or purging compound is introduced, thus eliminating positive conveyance until the barrel is completely full again. The only good reason to empty a barrel of material is immediately before the screw is to be pulled.
You should always keep the barrel full of material at all times. The best practice is to use a mirror to view the feedthroat and stop purging once the screw flights are fully visible. At this time, introduce the new material so that the barrel remains full of material at all times.
You should always ensure that the barrel is full of safe, heat stable material whenever the machine is to be shut down or stopped for any period of time. If you are running an unstable material, you should always have a safe, heat stable, material nearby available for use at a moments notice.
There are many other important aspects to proper and efficient purging, but maintaining a full barrel is critical.