How can I fix an unintended hole in my mesh? I've created a hollow object with a Boolean Difference, but it has left a hole in the mesh that I can't seem to fix. There are no vertices on the periphery of the hole itself, and it extends across two faces at right angles to each other.

When I look inside the hollow (as far as I can), I see that there are "shadow" connections between vertices that I would have expected to be unrelated.

I've tried manually reducing the NGON faces to quads and triangles, but it's had no effect on the hole. I've tried Mesh > Cleanup > Fix Holes, also with no effect. I've tried to Beautify the affected faces, again with no effect.

I've attached a link to the file in a state prior to my messing around trying to fix it (approx. 10MB)

Link to the .blend file, approx 10MB
There is no hole in the mesh, but a non-planar n-gon (a polygon with more than 4 vertices) that is ovelapping on top another face.

You should delete it and try to reconnect the remaining geometry using quads...