I’m open to any program that could fix this, but so far I haven’t found one that will. 3D scanners have a hard time seeing into a hole. That leaves pairs of naked edges that need to be bridged. Every app I’ve tried wants to constructs a cap on each edge which removes the pocket hole.
3D Coat does well with meshes, but won’t let me manually start the bridge. Rhino lets me start a bridge, but isn’t as reliable for filling holes. Either way, it’s a time-consuming process and there are a lot of holes. I need a mesh loft that lets me quickly select pairs of edge loops.