In power systems, the programmable numerical differential relays are widely used for the protection of generators, bus bars, transformers, shunt reactors, and transmission lines. Retrofitting of relays is the need of the hour because lack of proper testing techniques and misunderstanding of vital procedures may result in under performance of the overall protection system. Lack of relay’s proper testing provokes an unpredictability in its behavior, that may prompt tripping of a healthy power system. Therefore, the main contribution of the paper is to prepare a step-by-step comprehensive procedural guideline for practical implementation of relay testing procedures and a detailed insight analysis of relay’s settings for the protection of an Extra High Voltage (EHV) auto transformer. The experimental results are scrutinized to document a detailed theoretical and technical analysis. Moreover, the paper also covers shortcomings of existing literature by documenting specialized literature that covers all aspects of protection relays, i.e., from basics of electromechanical domain to the technicalities of the numerical differential relay covering its detailed testing from different reputed manufacturers. A secondary injection relay test set is used for detailed testing of differential relay under test, and the S1 Agile software is used for protection relay settings, configuration modification, and detailed analysis.