[Freesurfer] -autorecon2-cp

Hi, I have a general question about control points. I have added control points to fix the white matter boundary errors throughout the brain. I think that some of these control points that were placed in brain lesions (lower intensity voxels or black spots that are supposedly white matter) have changed the overall intensity and boundaries of the structures. I would like to remove some of these control points but they have gone through several iterations of recon already. Would removing the control points at this point and running -autorecon2-cp set the intensities back to original (orig.mgz)? Or should I go back and fix them from scratch?

Thanks, Jaiashre.