A new methodology for the statistical inference of the Equivalent Initial Flaw Size distribution (EIFSD) using the Dual Boundary Element Method (DBEM) is proposed. As part of the inference, Bayesian updating is used to calibrate the EIFS based on data obtained from simulated routine inspections of a structural component from a fleet of aircraft. An incremental crack growth procedure making use of the DBEM is employed for the modelling of the simultaneous growth of cracks in the structure due to fatigue. Multi-fidelity modelling, in the form of Co-Kriging, is used to create surrogate models that act in place of the DBEM model for the expensive Monte Carlo sampling procedure required for the statistical inference of the EIFSD. The proposed methodology is applied to a numerical example featuring a long fuselage lap joint splice in presence of multiple site damage (MSD). Results show that the EIFSD can be accurately estimated with data from 50 inspections. The employed Co-Kriging models proved to be effective substitutes for the DBEM model, providing significant reductions in the computational cost associated with the implementation of the proposed statistical inference methodology.