afni.nimh.nih.gov

SurfToSurf won't flip the data for you, so you would have to flip the surfaces separately. At that point, you could use SurfToSurf to map data from one surface to another similar surface or 3dVol2Surf to map data from a volume onto the flipped surface. There will be important differences between a left and right surfaces with one of them flipped, so the match won't be exact.