So tracing down further, the most problematic wires are the ones shown in the image. In the tree they show up as cable/bundle segments and cable locations. The image is just a snippet to show an example. In the main window I can't even click on and select the wire, like if I click on it, it doesn't highlight or anything. So I'm not sure if those are handled differently, or generate on the fly, but that seems to be the primary issue. I don't think the skel.part stuff ended up being anything when I searched down deeper. I'll keep working on the sweeps to see if I can add any info on that front but these wires seem to generate the most problems.