Luckily this is hard to notice for the average user, I will prioritize other issues first.
The only way to fix this is if I could make specific half shafts rotate or not rotate within a ponder or if I got them to delete in a ponder the same way they do when the brass gearbox isn't in a ponder (idk why it doesn't in a ponder but I guess that's just because of the way ponders render unfortunately. Hopefully this is fixed in a future flywheel update if I can't find a fix on my side)