Pilot flames, created by additional injectors of pure fuel, are often used in turbulent burners to enhance flame stabilisation and reduce combustion instabilities. The exact mechanisms through which these additional rich zones modify the flame anchoring location and the combustion dynamics are often difficult to identify, especially when they include unsteady hydrodynamic motion. This study presents Large Eddy Simulations (LES) of the reacting flow within a large-scale gas turbine burner for two different cases of piloting, where either 2 or 6 percent of the total methane used in the burner is injected through additional pilot flame lines. For each case, LES shows how the pilot fuel injection affects both flame stabilisation and flame stability. The 6 percent case leads to a stable flame and limited hydrodynamic perturbations in the initial flame zone. The 2 percent case is less stable, with a small-lift-off of the flame and a Precessing Vortex Core (PVC) in the cold stabilisation zone. This PVC traps some of the lean cold gases issuing from the pilot passage stream, changes the flame stabilisation point and induces instability.