I have also realized that even if you could get Grasshopper to bridge the hole, you would then very likely have the needed Boolean subtraction of a copy of the original mesh FAIL, since the surfaces of the original and patched meshes are coincident or nearly so, which destroys Booleans in Rhino.

Free Autodesk MeshMixer ( http://www.123dapp.com/meshmixer ) can also make a patch though, by selecting and deleting the edges of the hole then just using its Analysis automatic fixing feature to patch the two holes, the upper surface hole and the lower surface hole, by simply clicking on the spheres at the end of lines indicating each hole.

Then a Boolean difference does work, and unlike Rhino, instead of just failing, it leaves stray mesh faces here and there that can be deleted:

MeshMixer is a fun and rapidly improving program, worth learning the quirks of. There's no good update of the user manual though, but lots of YouTube videos and this course that is now on udemy:

https://www.kickstarter.com/projects/1727665673/3d-printing-toolkit...

The idea that you will automatically patch that hole via Grasshopper is utopian since it has two surfaces it needs to make, of a matching thickness apart. I thought of shrink wrapping with Kangaroo the whole form, but it wasn't working well, even if I saved the mesh from spreading out too much over the whole by adding a spring length restraint.

But! If you first manually isolate the edge of the hole by overlapping it with new geometry you create in order to define the overlap as a selection, or by drawing two loops on the surface, then you can simply split the mesh to isolate the hole edge from the body, and then just figure out how to cap the hole edge on both top and bottom sides, thus avoiding any failure-prone Boolean subtraction strategy. The perfect joint information is already there, being the original mesh along the hole edge.

Isolate and extract the edge manually, by modeling a surface or mesh surface through the form and splitting the form with it, then create a closed mesh solid from that ribbon-like loop of mesh surface.

In Autodesk MeshMixer, there is a vastly superior way to fill the hole, after deleting the edge of the hole. Instead of using the Analyze automatic patching command, once you delete the hole edge, you double click the edge within the Select palette to select the edge triangles, and then use the normal Erase & Fill command, and that gives TANGENCY instead of a dumb flat patch. However, the bottom patch then domes up through the top one, so you have to manually edit it back down, which is rather easy though. Or there is a Bulge option for the Erase & Fill that prevents it in the first place by bulging both patches out into space:

It's not very robust though, often giving bad artifacts after the Boolean and my attempt to then clean it up of stray stuff. I get double surfaces suddenly appearing, lots of crashes after very long delays. This would take quite some tweaking to develop a good workflow, and maybe require a few MeshMixer updates in the future to work better.