Well, This happens from time to time. If you deleted half of your mesh, did your work in maya, then mirrored and welded the halves back together, Maya renames this mesh. That is why the window prompt opens, because it has renamed the mesh. So you follow the directions and send it back to Z, and when the reproject happens, zbrush masks the mesh, except where you changed the topology. What I do is smooth out the areas that did not project well. Go from highest to lowest, and then back again. It is a pain, but not a huge one. Something you might try when you are using goZ and know you will be making changes is this; before sending the mesh to Maya, duplicate the mesh. Rename the copy something unrelated to the original name, like safety, or copy. Send the original to Maya and do your changes. When the mesh comes back to Maya, and you have this type of distortion, reproject the mesh onto the copy. Works every time.