No Ben
You need to fix those areas so zbrush checks it as a good mesh then project onto the good mesh, I am sure its the bad mesh that is the issue, try the zbrush integraty test on your mesh at the moment. The problem I had was a little tab of a poligon(non manfold geo I think they call it) If I new about it a clean up in maya would have been simple, only spotted in the UVs in maya...........dave