For the purposes of simplicity, I'd like to delete some joints on a figure before APEX rigging it. While deleting the actual joints is easy enough, that leaves all the geometry unweighted, and I have no idea what to do about that. This figure has two joints per toe; how would I go about re-weighting all of the toes to the parent ball joint?

I think if you used the "fbxcharacterimport" and delete the same joints with a "deletejoints" SOP on both the capture- and animated pose , you'll only lose the weighting of the deleted joints.

You can then use a "jointcapturepaint" to assign a different joint to the points that lost weighting.

The Capture Correct SOP should work I think to fix the skinning weights. Turn off Delete Stale Regions and then put in explicit joint names separated by spaces. It'll renormalize by default, so the old weights they used we be proportionally redistributed to the remaining weighted joints. However, if there were points that were only weighted to deleted joints, then you'll need to either paint them again or recompute them as mentioned.