I remove components while in schematic mode. I save it and even restart KiCad. I then regenerate the association by using .pro but the components are still in the .pcb file. How does one remove these components?
You need to export the netlist and re import it into pcb new.
In the import dialog you need to select delete under the extra footprints section.
(Disclaimer screenshot taken in kicad nightly. Small details might be different in the stable release.)
Thank you very much.