Faulted phase identification is one of the segments of conventional system protection that is severely vulnerable in the presence of inverter-based resources (IBR) such as Type IV wind and solar PV power plants. The work presented in this paper investigates the effect of IBRs on the conventional phasor-based faulted phase identification methods widely implemented in contemporary commercial protection relays using theoretical analysis and simulation results. Moreover, this premise is further validated by testing commercial line protection relays using hardware-in-the-loop simulations. This paper also evaluates the applicability of recently proposed transients/incremental quantities-based techniques to overcome the deficiencies of conventional methods to correctly identify the faulted phase in systems with IBRs through real-time and control hardware-in-the-loop simulations. Comparisons with commercial relays show that transient/incremental quantities-based methods are more suitable for systems with a high penetration of IBRs.