I found an issue working on 5.1.2-2 (W7).
When i remove footprint association to a particular component from the schematic footprint assignment dialogue box.
Later applying the update from PCB from schematic . The disassociated footprint doesn’t get removed from the pcbnew and it also remains with the airwires.
If you just unassign the footprint then you will get an error message in the update from schematic step. This error will prevent the tool from doing anything. Asign a reference that starts with # to tell kicad that a symbol should not be included on the pcb.
I am however not even sure your workflow is a good idea. Why include something in the schematic if it should not be on the PCB. (as a footprint/traces) Normally one would include such a thing in the pcb but mark it as “do not place”. (allowing for adding of functionality by simply soldering in these additional parts.) Solderjumpers or 0 ohm resistors might be necessary to limit negative impact while the subcircuit is not placed.