when I press the “reconstruct higher subdiv” button under the “Geometry” menu the geometry is cleaned up, however the eye area gets all screwy. The geometry spikes out in different areas. Anyone know the cause of this? or a way to fix this?
Thanks if you can help. 
Please post screen shots.
projections usually cause this type of error when working near an open edge, or two conflicting normal directions.
store a morph target at the highest subD before the reproject.
after the reproject grab the morph brush and you can push those areas back to where they were.