Local rock-dumping protection (RDP) can modify the evolution of pre-existing scour pits around subsea pipelines. This study combines field bathymetric surveys with REEF3D simulations to examine post-protection scour at a pipeline in the East China Sea. The Reynolds-averaged Navier–Stokes model couples a k-ω turbulence closure with sediment transport and bed evolution and was validated against Mao’s pipeline scour experiment. Four field-derived cross-sections were simulated under constant unidirectional inflow at a range of 0.5–2.0 m/s for 30,000 s. Field surveys showed that erosion shifted downstream after RDP, with its distribution varying with downstream slope-toe coverage and the transition to the surrounding seabed. The simulations indicate that the pre-existing scour pit and rock-induced bed mounds jointly reorganize flow separation and recirculation, helping to explain this redistribution. Stronger inflow produced greater lowering of the minimum bed elevation, reaching a range of 0.65–1.24 m at 2.0 m/s after 30,000 s. Continued lowering at the representative section late in the higher-velocity simulations highlights the influence of flow duration. The findings provide a physical basis for positioning remedial RDP relative to existing scour pits and for extending monitoring to potential erosion zones beyond the protected area.