Energization of a transformer results in sudden flow of current which is an effect of core magnetization. This current will be dominated by the presence of second harmonic, which in turn is used to segregate fault and inrush current, thus guaranteeing proper operation of the relay. This additional security in the relay sometimes obstructs or delays differential protection in a specific scenario, when the 2nd harmonic content was present during a genuine fault. This kind of scenario can result in isolation of the transformer by Buchholz and pressure release valve (PRV) protection, which is acted when fault creates more damage in transformer. Such delays involve a huge impact on the insulation failure, and chances of repairing or rectifying fault of problem at site become very dismal. Sometimes this delay can cause fire in the transformer, and this situation becomes havoc for a sub-station. Such occurrences have been observed in field also when differential relay operation was delayed by 10-15 ms by second harmonic blocking in some specific conditions. These incidences have led to the need for an alternative solution to eradicate such unwarranted delay in operation in future. Modern numerical relay, called as intelligent electronic device (IED), is embedded with advanced protection features which permit higher flexibility and better provisions for tuning of protection logic and settings. Such flexibility in transformer protection IEDs, enables incorporation of alternative methods such as dynamic switching of second harmonic feature for blocking the differential protection with additional security. The analysis and precautionary measures carried out in this case, have been simulated and discussed in this paper to ensure that similar solutions can be adopted to inhibit analogous issues in future.