Generally all normal transformer output should be checked by individual CT sets. If this recommendation is neglected, we must recheck the differential relay setting regarding to additional unchecked loads.
On the other hand the tertiary winding of an autotransformer, or three-winding transformer, is usually of much smaller kilovoltampere rating than the main windings. Therefore, fuses or overcurrent relays set to protect the main windings offer almost no protection to such tertiaries. During external system ground faults, these tertiary windings may carry very heavy currents.
The method selected for protecting the tertiary generally depends on whether the tertiary is used to carry load. If the tertiary does not carry load, protection can be provided by a single overcurrent relay connected to a CT on the tertiary winding. This relay senses system grounds and also phase faults in the tertiary or in its leads.
If the tertiary is used to carry load, partial protection can be provided by a single overcurrent relay supplied by three CTs, one in each winding of the tertiary and connected in parallel to the relay. This connection provides zero-sequence protection, but does not protect for positive- and negative-sequence overload current. The relay operates for system ground faults, but does not operate for phase faults in the tertiary or its leads. This relay needs to be set to coordinate with other system relays.