How to copy sections of layout

That approach might be OK. I’ll give it a try. I assume you mean this sequence:

  1. Start up PcbNew and do the append.
  2. Update the schematic, reannotate.
  3. Start up PcbNew from the launcher, update from schematic.
  4. Fix up the reference designators to match the schematic, and delete any new footprints the update from schematic brought in.