Frequency-based Substructure (FBS) is a widely used method in industries, allowing to obtain the dynamic characteristics of coupled systems from its uncoupled substructures. The dynamic characteristics of the uncoupled components represented by Frequency Response Functions (FRFs) can be obtained by measurements or simulation models. The FRFs at the interfaces of the components can be difficult to measure directly as it can be impossible to physically place sensors at a connection interface. Obtaining the FRFs of a virtual point from several measured locations becomes an important process to overcome this problem, known as Virtual Point Transformation (VPT). However, the unavoidable sensor orientation errors could cause inaccuracy in this process. First, these errors lead to non-reciprocal inaccurate interface FRFs. Second, matrix inversion of the interface matrix in the FBS coupling process amplifies these errors. To solve this problem, a correction method is proposed to apply on measured data with orientation errors on both input and output. The objective is to identify and correct these errors and thus improve the reciprocity of the interface FRFs. As a validation, tests have been performed on a typical passenger vehicle tire. By applying the proposed method to the measured data, the reciprocity of the interface matrix is significantly improved.