Normally the syncronisation between the schematic and the PCB is maintained via "timestamp" vlaues (will change to: "UUID" in KiCad V6).
If you do a copy and paste schematic symbols this information is lost.
To repair this, you have to use the same RefDes values in the schematic as the old symbols, and then while updating the PCB use the function "Match Method / Re-associate footprints by reference"
Another way to fix it is to draw a short track segment from the attachment point of pin 1 of each old Footprint, then delete the old Footprints, grab the new one by pin 1 and move it to the endpoint of the track.