The statistical inference of the Equivalent Initial Flaw Size Distribution (EIFSD) is developed for the first time using the Dual Boundary Element Method (DBEM) for assembled shear deformable plate structures. As part of this inference procedure, Bayesian updating is employed to enable the continuous refinement of the EIFSD via data obtained by many simulated routine inspections of a stiffened panel from a fleet of aircraft. Fatigue crack growth is modelled using an incremental crack growth procedure that only requires modelling of the boundary of the 2.5D structure with line elements and requires no remeshing during crack growth simulations. Stochastic Kriging is employed to account for the stochastic nature of fatigue crack growth and to offset the high computational cost associated with modelling complex built-up structures. To demonstrate the efficiency of the proposed inference methodology, a numerical example featuring a stiffened panel subjected to complex loading in the form of combined tension and bending is presented. Once the EIFSD has been inferred, it can be used to optimise the intervals between routine aircraft inspections via the use of reliability analysis techniques as part of a combined reliability-EIFS approach. It is demonstrated that the proposed methodology offers the capability to reduce the costs associated with inspections.