Just make a selction of some footprints and tracks, copy it to the clipboard, and paste it in another KiCad instance. For my previous post I tested this to copy from a “standalone” version of the PCB editor, into a project and it just worked as expected.
I would turn this around.
If you have a discrepancy between footprints, (for example when the link between schematic and PCB is lost) then you can first copy or move the PCB tracks, delete all the footprints, and use the endpoints of the remaining tracks to snap newly imported footprints to. This insures their correct relative position.
I’ve done this a bunch of time whilre reverse-eingineering a KiCad project from Gerber files. See: