Do you mean that they don't show up in the actual profile, and that's what you look at when deciding what sections to delete?
I have two suggestions:
1) When adding categories to profiles, keep them all together, either at the very top or at the very bottom of the profile.
2) When cleaning up profiles (so what you're actually asking about), first, look on the profile page to see what categories are there. Then, in the edit box, add those categories to the top or bottom of the edit box (or if you see them, just move them), then proceed with your cleaning up.