The dynamic properties of modern products are analysed using an experimental approach through the measurement of frequency-response functions (FRFs). For an individual measurement, the coherence offers an online check during the system acquisition. More general tools for determining the consistency of the complete measurement set are based on a comparison of the FRFs or the modal shapes with a numerical model. They are useful tools, but they rely on a comparison with a numerical model that might not reflect the behaviour of the actual system. This paper aims to develop a comprehensive experimental method to check the consistency of individual measurements based on comparisons with the complete experimental response model. The numerical model is introduced only to enable the experimental model to be expanded using the System Equivalent Model Mixing method. The entire formulation is developed in the frequency domain, so that the transition to the modal domain, which might remove the physically relevant information from the system, is not required. In the frequency domain, it is possible to assess the consistency of the FRF across the entire frequency range of interest and not only in the region of the natural frequencies. This is of great importance in the area of frequency-based substructuring, where even small inaccuracies in the substructure's FRFs (e.g., the position of the anti-resonance) can lead to erroneous coupling results due to the inversion process. The experimental case study demonstrates the efficiency of the proposed approach. By removing the identified inconsistent measurements, it was possible to significantly increase the accuracy of the final coupling process.