So, I had merged several organic meshes together via boolean union, and then used the Remesh modifer. However, Remesh seems to be creating a bunch of holes in the mesh. I tried cleaning them up with sculpting mode, but it just seems to crunch them together without really getting rid of them, and in some cases results in non-manifold geometry.
Well, that gives me a good start to go on. Although I’ve already saved after applying the booleans, I do have the MeshLint addon enabled, which automatically tracks down non-manifold elements.
And the organic meshes I had merged were some cave and rock “sculpties” obtained from Second Life, so I am quite certain that bits of them may be non-manifold.
Okay, turns out the meshes were just Joined rather than Boolean Union’ed, which I had done initially. That means I can go through and fix the mesh pieces before doing the boolean.