So I had to do a bunch of hand editing to a terrain due to a large canyon causing all sorts of troubles with TGEA. Basically if your terrain slopes over about 80 degrees it will form a terrain hole nearby. So in order to fix the problem I wound up loading up sapphire and hand editing the terrain making sure slope of the areas where I found holes were adjusted. However to do this I had to destroy much of the existing terrain detail such as erosion paths.
What would be a nice feature is to once you edit the terrain in sapphire you can use the select area tool, highlight an area of the map (presumably where you made changes), and have it merge your changes to the height map into the existing design map detail settings. The main contour of the terrain would follow your changes but would still be reprocessed again taking into account the design map. This would add back in some of the terrain realism to areas hand edited which usually come out looking flat and unnatural