“Orthogonal” is a term used to describe two vectors that are perpendicular (at 90 degrees) to each other. In 3D space, when the X, Y, or Z-axes are not perpendicular, they are considered “non-orthogonal” and the FBX plug-in does not support their representation as a matrix. For example, a non-orthogonal set of axes can occur when you use rotation and scaling to skew an object.
Because the FBX plug-in assumes that there is always a 90 degree angle between the X, Y, and Z axes, it can support only orthogonal matrices. Any transformed axes that have non-orthogonal TRS matrices are ignored by the FBX plug-in, so it does not import or export effects created when axes are not orthographic. Because of this, any non-orthogonal effect (such as skewing) is lost.
This can cause problems even when you have transformation data that has been inherited from other objects, for example, scaling via a parent object where the result is a non-orthogonal local TRS matrix.