John Doyle
Ansys Employee

The input data (from Moldflow) is parsed, and then transferred to the downstream Mechanical System, where it can be applied in the form of element orientations, material fields and initial stresses.  

Please refer to Workbench User's Guide=>Working Through a System=>Component Systems=>Injection Molding Data.  This section of the online docs offers some commentary on Fiber Orientation Tensors and Fiber volume fraction mapping.   It would seem, from this section of the docs, that the assumption is that the two geometries are the same.  With different geometries, I am not sure this even works, but if the region fwithout fiber info is very large (relative to element size), I would not expect it to work very well.