There is the original model. From it was made the animation (morphing, just move the vertices). It is used to animate MeshMerpher. When you import a model of two frames (Noramls and tangents - calculate and smooth angle - 180) showed that the peaks kolichesvto the same, but different kolichesvto tris (1260 and 1257) (triangles)! And because of this coincidence of MeshMerpher breaking model for animation. Question: Why does the import kolichesvto different triangles? occurred only after the movement of vertices, and all of the original model.
What system are you using for the morphing in Unity, maybe it is altering the data.
The different number of imported models i see on mesh in Unity. (tris).
For morphing I’m using this: http://www.unifycommunity.com/wiki/index.php?title=MeshMorpher
Sound like your 3d package exporter is either removing degenerate tris or when you modelled up the 2nd mesh you managed to change the tri count. I would suggest using one of the other Morphing systems available on the asset store preferably one that has an exporter for your 3d package or one that at least deals with the different vertex counts for you. The wiki script is a bit limited on its features and user friendliness as well as its docs and support.