The "beacon zone" is the immediate zone around your base station. When your pet is within the beacon zone, your tracker goes into low power mode. We do this as we know that your pet is safely within the Whistle zone and cellular connection is hence not required.
If your pet leaves the beacon zone, you can then use both the Refresh GPS and Track features to locate your pet (even if this is still within your Whistle zone). As an indication, the beacon zone area is typically a radius of 50 meters from the base station and your pet has to be outside of this area for a few minutes (but within the Whistle zone) to be recognized as being out of the beacon zone.