The physical mechanism leading to flame local extinction remains a key issue to be further understood. An analysis of large eddy simulation (LES) data with presumed probability density function (PDF) based closure (Chen et al., 2020, Combust. Flame, vol. 212, pp. 415) indicated the presence of localised breaks of the flame front along the stoichiometric line. These observations and their relation to local quenching of burning fluid particles, together with the possible physical mechanisms and conditions allowing their appearance in LES with a simple flamelet model, are investigated in this work using a combined Lagrangian-Eulerian analysis. The Sidney/Sandia piloted jet flames with compositionally inhomogeneous inlet and increasing bulk speeds, amounting to respectively 70 and 90% of the experimental blow-off velocity, are used for this analysis. Passive flow tracers are first seeded in the inlet streams and tracked for their lifetime. The critical scenario observed in the Lagrangian analysis, i.e., burning particles crossing extinction holes on the stoichiometric iso-surface, is then investigated using the Eulerian control-volume approach. For the 70% blow-off case the observed flame front breaks/extinction holes are due to cold and inhomogeneous reactants that are cast onto the stoichiometric iso-surface by large vortices initiated in the jet/pilot shear layer. In this case an extinction hole forms only when the strain effect is accompanied by strong subgrid mixing. This mechanism is captured by the unstrained flamelets model due to the ability of the LES to resolve large-scale strain and considers the SGS mixture fraction variance weakening effect on the reaction rate through the flamelet manifold. Only at 90% blow-off speed the expected limitation of the underlying combustion model assumption become apparent, where the amount of local extinctions predicted by the LES is underestimated compared to the experiment. In this case flame front breaks are still observed in the LES and are caused by a stronger vortex/strain interaction yet without the aid of mixture fraction variance. The reasons for these different behaviours and their implications from a physical and modelling point of view are discussed in this study.