Is it becoming black? or is it becoming transparent? If there is a negative scale, It is possible that when your freeze transform, it is reversing the normals. If you then have backface culling on, you won't be able to see faces who's normals are pointing away from you.

Alternatively, it may be disconnecting those faces from the rest of the mesh. this is also an issue with having the face normals facing the opposite direction then the face normals of those faces adjacent to them.

You can fix ether of these issues by selecting the mesh, going to Display > polygon > Face normal (this displays the normals), then select the faces that are facing the wrong way and, in your polygon menu set, select Normals > reverse.

you can then go to Display > polygon > Custom polygon display, and check on border edges. this will make any edge that is not connected to another edge appear to be thicker. check around the problem area to see if any of your edges are thinker, if they are, your going to have to merge the verts back together, then clean up your UV's.

Good luck, hope this helps.