What is the difference between Average Reference and Common Reference Mode?

In Average Reference Mode all unipolar channels are referenced to the average, whereas in Common Reference all unipolar channels are amplified against an additional REF electrode.

The Reference Mode is set by the user via the application software interface. In case the device is configured for Average Reference measurement, all signals are amplified against the average of all connected unipolar inputs. Inputs that are not connected to an electrode are automatically switched off.

In case the device is configured for Common Reference measurement, the unipolar inputs are referenced against the electrode connected to the REF input. Therefore, the main difference is that an additional REF electrode is connected to the device to which all channels are referenced. 

Average Reference is recommended, for EEG, as it does not depend on a separate reference electrode and location of a reference electrode. However, for HD-EMG applications the Common Reference configuration is preferred. The final decision about the measurement setup is left to the researcher.