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SQUID technology has recently evolved to the point that it can be used for industrial applications in Non-Destructive Evaluation (NDE). We present the implementation of an HTS SQUID magnetometer in an eddy current testing system to measure very thick structures in large aircraft. We measured a 62 mm-thick, bolted aluminum sample from the EADS-Airbus, similar to the three-layered outer wing splice that is being proposed for the Airbus A-380. The combination of field sensitivities of a few pT/√Hz and a large dynamic range of about 140 dB/√Hz enabled us to detect defects at a depth of up to 40 mm. However a problem was presented by the fact that deep-lying defects which caused small field variations were superimposed on field changes, in their turn caused by current distortions in the vicinity of the titanium bolts. Separation of these two contributions was achieved through parameter optimization based on FEM simulations and signal processing. We report on the possibilities for flaw detection using adapted eddy current excitation.